From my Tome of House Rules v1.54

A note on symbols:

* designates an element I am not happy with and requires further work
** designates a change that is largely based on flavor and setting, instead of balance reasons.

PHB

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-Natural Spell is banned.
-You may take a ‘skill feat’ that gives +2 to two skill checks and apply it to a skill set instead of two separate skills. Alternately, you may select another type of skill check along the same theme. You gain the benefit for that type of check as well. This other skill may not be Spellcraft, Use Magic-Device or Concentration.
-Combat Casting grants a +5 bonus.
-Combat Expertise allows the subtraction of any value from attacks rolls, limited only by BAB.
-Combat Reflexes allows you to make Attacks-of-Opportunity while flat-footed (but you must be aware of your opponent). This does not make you not flat-footed; it is not Uncanny Dodge.
-Dodge works on any opponent, as long as you are aware of them prior to the attack. For supporting Feats or abilities that work off of Dodge, you must still declare an opponent for those abilities.
-*Endurance Grants +2 HP and allows you to move your normal speed despite encumbrance, in addition to normal benefits. It now has “Con 13+” as a prerequisite.
-Far Shot no-longer has any prerequisites.
-Great Fortitude also adds +2 to Constitution checks (but not to Constitution-based skill checks or HD rolls)
-Iron Will also adds +2 to Wisdom checks (but not Wisdom-based skill checks)
-Lightning Reflexes also adds +2 to Dexterity checks (but not Dexterity-based skill checks or Initiative checks)
-Mobility also grants +8 to Tumble checks when tumbling to move past opponents.
-Quick Draw also allows you to sheath a weapon as a swift action.
-Quicken Spell has the prerequisite “Ability to cast 4th-level spells”.
-Improved Critical now stacks with Keen Edge, but not with any other effect or ability that may increase critical threat range (unless that ability explicitly states that it stacks).
-Skill Focus also makes the chosen skill a class skill for you, for all classes. Furthermore, it has “4 ranks in the selected skill” as a prerequisite, grants a +4 bonus to that skill and allows you to take 10 when performing it even while rushed or threatened.
-Weapon Focus grants +2 to hit with the selected weapon.
-Weapon Specialization grants +3 damage with the selected weapon.
-Greater Weapon Focus grants a further +2 to hit with the selected weapon, +4 to defensive Sunder or Disarm rolls involving the weapon and the ability to take 10 on attack rolls involving the weapon.
-Greater Weapon Specialization grants a further +3 damage with the selected weapon and doubles the weapon damage dice (1d8 becomes 2d8, 2d6 becomes 4d6, etc). Furthermore, you automatically succeed at critical confirmation rolls with the selected weapon.


Complete Divine

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-Divine Metamagic is Banned.
-Arcane Disciple is Banned.
-Lion’s Pounce has the added prerequisite of “two other Wild feats”
-Reach Spell only takes up a slot 1 level higher.
-**Sanctify Relic is removed.
-Serpent’s Venom lasts for 1 round (feat doesn’t specify a duration).
-Spontaneous Healer and Wounder are removed.
-True Believer grants you +4 to saves to avoid doing something contrary to your faith instead of the listed benefits. (generally something that would threaten to make you lose cleric/paladin standing)
-**Faith Feats will not be used.


Complete Arcane

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All feats that grant spellcasting ability (such as communicator) are removed from normal play. They may be allowed in very specific circumstances or character concepts.

Mage Slayer and its chain cannot reduce your caster level below 1 (that is to say, if you are a 1st-level caster with 3 Mage Slayer feats, your caster level is still 1).

-Born of the Three Thunders: Uses a spell slot 1 level higher.
-Cooperative Spell maxes out at 6 casters. If any of the casters are disrupted, the spell is lost. Add 2 to the DC of any Concentration check made by a casting using Cooperative Spell.
-*Craft Contingent Spell
-Delay Spell only uses a slot two levels higher.
-*Double Wand Wielder
-Draconic Claw does not allow you swift-action claw attacks.
-Draconic Flight grants you wings and poor manoeuvrability. It also lasts for 3 rounds per level of the spell.
-Draconic Heritage also grants you 2 ranks in Speak Language (Draconic).
-Draconic Power’s caster level boost functions only for the appropriate energy type. This is not a house rule.
-Draconic Skin increases your Natural Armor by 2.
-Extra Invocation can grant you knowledge of any grade of Invocation that you can currently know.
-Extra Slot may be of any level you can currently cast.
-Extra Spell can grant knowledge of any level of spell that you can currently cast.
-Extra Spell Secret is removed.
-Guardian Spirit is removed.
-Innate Spell uses a spell slot 7 levels higher then its base spell.
-Lord of the Uttercold: Uses a spell slot 1 level higher.
-Non-Lethal Substitution spells are still subject to the appropriate energy resistance. They take up a slot of the spell’s normal level.
-Pierce Magical Concealment also allows you to automatically succeed at Will Disbelief checks vs. Illusions, and you dispel Invisibility effects on a successful attack.
-Ranged Spell Specialization grants +3 damage.
-Sculpt Spell cannot be used with Anti-Magic Field.
-Sudden Quicken has the Prerequisites: Quicken Spell, any 2 Sudden Metamagic Feats.
-Touch Spell Specialization grants +3 damage.
-Wand Strike does 1d6 damage per spell level of the wand and burns 1 charge of the wand.


Complete Adventurer

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-Appraise Magic Value only takes 1 hour to perform.
-Brachiation is not usable in medium or heavy armor.
-Disguise Spell may not be used in conjunction with metamagic feats.
-Dual Strike attack penalties are reduced to -2 and -6.
-Extraordinary Spell Aim does not increase casting time.
-Goad effects all of the target creature’s attacks.
-Improved Swimming grants +4 to swim checks, in addition to stated benefits.
-**Insightful Reflexes is removed.
-Jack of All Trades allows you to use any skill as if you had a number of ranks equal to half your possible total of cross-class ranks in that skill for your level. For instance, at level 6, it would allow you to treat a skill you had no ranks in (such as Decipher Script) as having 2 ranks in that skill.
-Leap Attack: As part of a charge, make a DC 15 Jump check to spend 10 feat of your movement in the air. If you are only moving 10 feet total in your charge, increase the Jump DC to 20. The initial strike of your charge gains a total of +4 to hit and you deal an amount of additional damage equal to your strength modifier. However, you suffer a -4 penalty to AC. These effects replace the normal benefits and drawbacks from charging.
-Natural Bond may only be used to offset multiclassing penalties, not the adjustment to effective level imposed by having a more powerful animal companion.
-Using Subsonics increases your Perform check DC by 5.
-Tactile Trapsmith only allows you to use your Dexterity bonus on Search checks made to find traps.
-Lyric Spell only requires one use of your bardic music ability per spell level, instead of the 1 + 1/spell level as listed.
-Blindsense only lasts for 1 minute, not 1 minute/HD.
-Climb like an Ape lasts for 1 minute/HD, and grants all listed bonuses only during this duration.
-Cougar’s Vision lasts for 10 minutes/HD, and grants all listed bonuses only during this duration.
-Hawk’s Vision lasts for 10 minutes/HD.


Complete Warrior

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-Clever Wrestling has Improved Grapple instead of Improved Unarmed Strike as its prerequisite.
-Dash also works in Medium armor.
-Eagle Claw Attack also allows you to overcome the first 10 points of hardness of the object you attack.
-Extend Rage doubles the duration of your rage or frenzy ability.
-Extra Smiting BAB prerequisite lowered to 3.
-Eyes in the Back of Your Head does not stop people from flanking you, only removing the to-hit bonus. This is not a house rule.
-Faster Healing doubles the rate you naturally heal, instead of as listed.
-Freezing the Lifeblood BAB prerequisite lowered to 8+.
-Greater Kiai Shout is removed.
-Greater Resiliency can be taken more then once, its effects stack.
-*Hold the Line has Charge Breaker as it’s prerequisite instead of Combat Reflexes. It only functions if you have a weapon readied against a charge.
-Improved Combat Expertise is removed.
-Improved Favored Enemy also grants +3 to attack your favored enemies.
-Improved Rapid Shot doesn’t have Manyshot or Point Blank Shot as prerequisites, but does have BAB 3+.
-Improved Toughness does not have any prerequisites.
-*Karmic Strike
-Kiai Shout is removed.
-Monkey Grip now reads “You may wield weapons as if you were one size category larger. Thus, you do not suffer the normal -2 penalty to attack when wielding oversized weapons.” and nothing further.
-Phalanx Fighting does not require you to use a light weapon. If you are using a tower shield instead of a heavy shield, the bonuses the feat grants double to +2 static and +4 (with +2 to Reflex saves) when near another Phalanx Fighter, for a total bonus of +6.
-Pin Shield requires opposed melee attack rolls, you using your sword and your opponent his shield. Your opponent applies any enchantment bonus his shield has to AC as a bonus on his roll. BAB prerequisite reduced to 3+.
-Power Critical grants +8 to confirm, instead of as listed.
-Prone Attack doesn’t have Lightning Reflexes as a prerequisite, but its BAB prerequisite is increased to 5+.
-Ranged Pin is removed.
-Sharp Shooting reduces the bonus cover grants to AC by 2. Furthermore, it reduces less than full concealment by 10%.
-Weakening Touch allows a Fort save at your Stunning Fist DC.
-Divine Cleansing grants its bonus to all saves, not just Fortitude.
-Divine Vigor lasts for a number of rounds equal to your Charisma modifier (instead of minutes).
-Calvary Charger: With Leaping Charge, you may set your Ride DC at 30 or higher, granting +2 more to damage each time (thus +6 at DC 30).
-Formation Expert: Lock Shields grants +2 AC, instead of as written. Step into the Breach requires an unobstructed path to where your ally fell, instead of as written. Wall of Polearms also grants a +2 damage bonus to charging or mounted foes (+4 damage to charging mounted foes) under the indicated circumstances.
-*Raptor School: You may set your Eagle’s Swoop DC at 35 or higher, granting +2 more to damage each time (thus +6 at DC 35).
-Bear Fang Style has Improved Grapple instead of Power Attack as a prerequisite.
-Hammer’s Edge Style has Power Attack instead of Improved Bull Rush as a prerequisite.
-Three Mountains does not have Improved Bull Rush as a prerequisite.


New Feats:

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New Feats:

Pierce the Wind [General]

Prerequisites: BAB 8+, Point Blank Shot, Precise Shot, Far Shot, Strength 19+

Benefit: When firing in windy conditions, you may treat the wind as if it was two levels milder. This allows you to fire through a Wind Wall or similar effect.


Shield Mastery [General]

Prerequisites: BAB 3+, proficiency with shields.

Benefit: You gain double the base AC bonus from large and small shields. In other words, small shields now grant you +2 AC and large shields grant you +4.


Armor Mastery [General]

Prerequisites: BAB 10+, Armor Specialization, proficient with all types of armor.

Benefit: The AC granted by any armor you wear is increased by 2 and the Armor Check Penalty is reduced by 4. Furthermore, you gain Damage Reduction based on how heavy your armor is. Light armor grants DR 2/-, Medium armor grants DR 5/-, Heavy Armor grants DR 10/-. The DR granted by this feat does not stack with that granted by Armor Specialization.


Defensive Feint [General]

Benefit: When a character successfully feints an opponent, he or she may elect to forego the opponent becoming flat-footed against the next attack in favour of gaining either a +4 dodge bonus to AC or partial (20%) concealment against that opponent for the duration of the following round.


Improved Whirlwind Attack [General]

Prerequisites: Dex 13+, Int 13+, Combat Expertise, Dodge, Mobility, Spring Attack, Whirlwind Attack, BAB 9+

Benefit: You may use the Whirlwind Attack feat as a standard action.


Master Whirlwind Attack:

Prerequisites: Dex 13+, Int 13+, Combat Expertise, Dodge, Mobility, Spring Attack, Great Cleave, Whirlwind Attack, Improved Whirlwind Attack, BAB 11+

Benefit: The Whirlwind Attack feat may be used in conjunction with Great Cleave.


Maim [General]

Prerequisites: BAB 5+, Improved Sunder

Benefit: As a standard action, you may attempt to make a crippling attack. If your attack deals 10 or more damage, your target’s move speed is reduced to half. Your attack may be a melee attack or a ranged attack within 30 feet.

This reduction lasts until the subject heals an amount of damage equal to the original attack.


Improved Resistance

Prerequisites: Innate Resistance 4, Con 13+

Benefit: Your Innate Resistance value improves by 4.

Special: You may take this feat multiple times, its effects stack.


Persistent Resistance

Prerequisites: Innate Resistance 14, Con 15+

Benefit: Spellcasters must check twice to overcome your Innate Resistance, succeeding both times in order to effect you with a spell. If you have an ability that is bolstered passively by IR, it is also subject to this benefit.


Spell Ward

Prerequisite: Innate Resistance 11, Con 15+

Benefit: You gain +2 to all saves versus spells and spell-like effects.


Precision Strike [General]

Prerequisites: BAB 1+, Weapon Finesse

Benefit: On your action, before making attack rolls for a round, you may choose to subtract a number from all melee attack rolls and add that number to all melee damage rolls. This number may not exceed your base attack bonus. You must use a weapon that benefits from Weapon Finesse with this feat. The penalties to attack and bonuses to damage last until your next turn. Targets immune to precision damage (such as undead) are likewise immune to this effect.

Unlike Power Attack, the kind of weapon and how you wield it is irrelevant to the functioning of this feat; the only requirement being that you use a weapon you have taken Weapon Finesse for.

This feat cannot be used in conjunction with Power Attack or Called Shot.


Called Shot [General]

Prerequisites: BAB 1+, Point Blank Shot, Precise Shot.

Benefit: On your action, before making an attack roll, you may choose to subtract a number from your ranged attack rolls and add that number to your ranged damage rolls. This number may not exceed your base attack bonus. Targets immune to precision damage (such as undead) are likewise immune to this effect.

Your target must be within 30ft to benefit from this effect.

This feat cannot be used in conjunction with Power Attack or Precision Strike.


Pin Down [General]

Prerequisites: BAB 6+, Point Blank Shot, Precise Shot.

Benefit: As a full-round action, you may make a single ranged attack with a bow, light or heavy crossbow or medium-sized or larger thrown weapon against a ground based target within 60ft. If your attack hits, your opponent must make a Fortitude save (DC = 10 + damage dealt) or be pinned immobile by your attack, unable to move from that spot. Your opponents may still attack and defend themselves normally and this feat does not work on opponents more then two size categories larger then yourself.

This effect may be removed be a DC 20 heal check requiring a full-round action or by magical healing equal to the original damage of the attack. Otherwise it ends in 3 rounds as the weapon works itself free.
Alternately, the affected individual may attempt a DC 15 Strength check as a move-equivalent action to pull the weapon free. However, doing so results in 1d8 damage to the individual and reduces their movement by half (DC 15 heal check to remove this penalty, or magically healing the damage caused by pulling the weapon loose).
If an opponent is afflicted by more then one Pin Down effect, increase all DCs by 5 for each additional active effect.


Charge Breaker [General]

Prerequisite: Weapon Focus and Weapon Specialization (any weapon that does additional damage to a charging opponent, such as a longspear), BAB 3+.

Benefit: When you ready a weapon against a charge, you deal double damage (or triple damage with a spear). Furthermore, you gain +4 to hit a charging opponent.


Improved Weapon Finesse [General]

Prerequisite: Weapon Finesse, Precision Strike, BAB 3+

Benefit: You may add your Dexterity modifier to damage, instead of your Strength modifier.

Anti-Magic Specialist [General]

Prerequisites: Ability to cast Dispel Magic or Greater Dispel Magic, Spell Focus (abjuration), Spellcraft 5 ranks, Know (arcane) 5 ranks.

Benefit: Add 4 to your caster level check when you cast Dispel Magic or Greater Dispel Magic. Gain +2 to Spellcraft or knowledge (arcane) checks to identify an active spell or magical effect.


Linguistic Training [General]
Prerequisite: Speak Language 4 Ranks.

Benefit: Gain 5 class ranks in Speak Language, these may be spent on any number of languages.


Linguistic Specialization [General]

Prerequisites: Mastery (rank 5) of a language, Int 15+.

Benefit: While using a language you have Mastered in language-dependant spells or abilities, you gain a +2 bonus on your effective level (as considered by that ability). Furthermore, you gain a +2 bonus to your spell-save DCs on any language-dependant compulsions or enchantments you cast.


Linguistic Mastery [General]

Prerequisites: Mastery (rank 5) of three languages, Linguistic Specialization, Int 15+.

Benefit: Gain a +4 competence bonus on all language-dependant skills. This bonus stacks with that granted by Mastering a language.
Furthermore, Speak Language is always a class skill for you, and you may purchase Speak Language ranks at half the normal cost.
Finally, you may cast Comprehend Languages at will.


Quicken Skill [General]

Select a number of skills equal to 3 + character's Int modifier.
Prerequisite: 1 rank into each selected skill.

Benefit: The character can perform the selected skills in half the time if it requires more than a full-round action to perform. Skill uses requiring a full-round action are reduced to standard actions while skills requiring standard actions are reduced to move actions. Skill uses requiring move actions cannot be quickened.

Special: This feat can be taken multiple times. Its effects do not stack. Each time it is taken, it applies to a new set of skills.


*Disable Magic (rogue special ability)

Benefit: You can disable or bypass locks, traps or other obstacles or ongoing spell-effects made by magic using special dispel dust applied skilfully. The DC to Disable Device any particular effect is 25 + spell level. This removes the magic effect from as much as a 10ft area. You can use this ability against any ongoing magical effect that would be effected by Dispel Magic.

Poison Use (rogue special ability)

Benefit: You gain Safe Poison Use (as assassin).


Hide in Plain Sight (rogue special ability)

Benefit: You can make a hide check even while being observed (as ranger).


Feedback, critique and such encouraged.