Here is what i've come up with between episodes of Fringe. Feel free to take any or none of it -- its not complete, because I think you probably know best what skills you'd like and what bonus feats you think would be most applicable.
Mechanically, the thing is outright inferior to a rogue when it comes to attacking -- but it has a ton of options to wound enemies and can kill folks pretty early on. it also has some soft control options for some tactical ability. I specifically did not include any abilities that are explicitly supernatural, but I could probably come up with 10 more if you'd like some supernatural options: i just stuck as close to "sniper guy" as possible.
Keep in mind that the current wording allows you to stack multiple Art of War abilities, so you can Daze and Bleed a person in the same go, if you'd like.
The Sniper
Hit Die: d6
Skill Points: 6 + Int
Skills: ???
Table 1.1 – The Sniper
{table=head]Level|Base Attack Bonus|Fort Save|Ref Save|Will Save|Special|Sniper Shot
1st|+1
|+0
|+2
|+2
|Sniper Shot; Ranged Precision|+1d8
2nd|+2
|+0
|+3
|+3
|Bonus Feat|+1d8
3rd|+3
|+1
|+3
|+3
|Art of War|+1d8
4th|+4
|+1
|+4
|+4
|Bonus Feat|+1d8
5th|+5
|+1
|+4
|+4
|Art of War|+2d8
6th|+6/+1
|+2
|+5
|+5
|Bonus Feat|+2d8
7th|+7/+2
|+2
|+5
|+5
|Art of War|+2d8
8th|+8/+3
|+2
|+6
|+6
|Bonus Feat|+2d8
9th|+9/+4
|+3
|+6
|+6
|Art of War|+3d8
10th|+10/+5
|+3
|+7
|+7
|Swift Sniper Shot|+3d8
11th|+11/+6/+1
|+3
|+7
|+7
|Bonus Feat|+3d8
12th|+12/+7/+2
|+4
|+8
|+8
|Art of War|+3d8
13th|+13/+8/+3
|+4
|+8
|+8
|Bonus Feat|+4d8
14th|+14/+9/+4
|+4
|+9
|+9
|Art of War|+4d8
15th|+15/+10/+5
|+5
|+9
|+9
|Bonus Feat|+4d8
16th|+16/+11/+6/+1
|+5
|+10
|+10
|Art of War|+4d8
17th|+17/+12/+7/+2
|+5
|+10
|+10
|Bonus Feat|+5d8
18th|+18/+13/+8/+3
|+6
|+11
|+11
|Art of War|+5d8
19th|+19/+14/+9/+4
|+6
|+11
|+11
|Bonus Feat|+5d8
20th|+20/+15/+10/+5
|+6
|+12
|+12
|One Shot, One Kill|+5d8[/table]
Sniper Shot (Ex): As a move action, you may designate one target you can see as your “mark”. The next successful attack you make against your mark inflicts additional damage as listed on Table 1.1. If your mark is flat-footed, maximize the damage inflicted by a successful attack. Successfully attacking your mark ends the “mark” status.
You may only have one mark active at a time. Choosing a new mark automatically cancels the effect on the previous mark.
At 10th level, you may choose a mark as a swift action.
Ranged Precision (Ex): When you make an attack with a ranged weapon, add your dexterity modifier to the damage inflicted by that weapon. Additionally, you double the range increment of any ranged weapon you use.
Art of War (Ex): The Sniper is a living weapon who uses incredible skill to strike even the most well-protected enemy from vast distances. Because each Sniper is shaped by the war he fights, every sniper has unique training and special “tricks” they use to survive a life of constant conflict. These knacks play to a Snipers strengths, creating one of the most versatile and deadly combatants on the field.
Spoiler
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Tactical Positioning (Ex)
Requires: None
Effect: Whenever you hit your mark, you may move up to half your speed. This movement
does not provoke attacks of opportunity.
Death Attack (Ex)
Requires: Dexterity 18+; Sniper Level 7
Effect: When you successfully damage your mark, you may sacrifice sniper shot dice to
make your attack a Death Attack. An opponent who is struck by a death attack must make
a Fortitude Save (DC 10 + ˝ Sniper Level + Dexterity modifier) or be instantly slain. An
opponent who successfully saves against this effect takes normal damage, but cannot be
targeted by Death Attack again for 5 rounds.
The number of dice that need to be traded to activate a death attack depends on the Hit
Dice of the opponent you are attacking:
1-6 HD: 1 die
7-12 HD: 2 dice
13-18 HD: 3 dice
19-24 HD: 4 dice
25+ HD: 5 dice
Opponents who are immune to your Sniper Shot are also immune to your death attack.
Breaching Shot (Ex)
Requires: Dexterity 16+; Sniper Shot 1d8
Effect: When you successfully hit your Mark, you may trade away 1 sniper shot die to
ignore any damage reduction possessed by the target for the purpose of this attack.
Kneecapper (Ex)
Requires: Sniper Shot 1d8
Effect: When attacking your Mark, you may trade 1 sniper shot die to attempt to entangle
your opponent. Your opponent is entitled to a Reflex save (DC 10 + ˝ Sniper level +
Dexterity modifier) to resist the effect. On a failure, your opponent is Entangled for 1d4 rounds.
Dazing Shot (Ex)
Requires: Dexterity 16+; Sniper Shot 2d8
Effect: When you successfully hit your Mark, you may trade 2 or more sniper shot dice to
attempt to Daze your opponent. Your opponent is entitled to a Fortitude save (DC 10 + ˝
Sniper level + Dexterity modifier) to resist the effect. On a failure, your opponent is Dazed for 1 round + 1 additional round for every Sniper Shot die beyond the second you traded away to activate this ability.
Chained Sniper Shot (Ex)
Requires: Dexterity 16+; Sniper level 12
Effect: When you successfully attack your Mark, the target does not immediately lose the Marked status. Instead, your next attack against that target inflicts 1 fewer die of Sniper Shot damage than it normally would. Each successful attack reduces the Sniper Shot dice by 1 until you miss, or until you use all of your attacks.
Ending your round of missing an attack ends this effect.
Killbox (Ex)
Requires: Sniper level 5
Effect: As a swift action, you may designate a 10 foot radius within your weapons first range increment as a Killbox. You threaten these squares as if you were making melee attacks into those squares. While this ability is active, you cannot make attacks of opportunity against squares you would normally threaten.
Improved Killbox (Ex)
Requires: Killbox
Effect: When you activate Killbox, increase the threatened radius to 15 feet. Additionally, you can set the Killbox anywhere within your weapon’s second range increment.
Bleeding Wounds (Ex)
Requires: Sniper Shot 1d8
Effect: When you hit your Mark, you may trade 1 or more Sniper Shot dice to inflict a bleeding wound on your target. The target loses 2 hp per round for every Sniper Shot die you trade to use this effect. Every die traded beyond the first increases the DC of the Heal check by 2.
Deadly Wound (Ex)
Requires: Sniper Shot 1d8
Effect: When you hit your Mark, you may trade 1 or more Sniper Shot dice to inflict ability
damage on your target. Your opponent is entitled to a Fortitude save (DC 10 + ˝ Sniper
level + Dexterity modifier) to negate the effect. On a failed save, the opponent takes 2
points of ability damage to the attribute of your choice for every Sniper Shot die traded.
Piercing Shot (Ex)
Requires: Sniper level 5
Effect: As a full action, you may make a 50 foot line attack anywhere within the first
range increment of your weapon. Your opponent is entitled to a Reflex save (DC 10 + ˝
Sniper level + Dexterity modifier) to negate the effect. On a failed save, the opponent
takes normal weapon damage.
Ricochet Attack (Ex)
Requires: None
Effect: You can ignore the effects of partial cover and standard cover against enemies you
attack. Against your Mark, you can ignore improved cover.
Staggering Attack (Ex)
Requires: None
Effect: When you hit your Mark, you can trade 1 die of Sniper Shot damage to render your
opponent flat-footed against the next attack that strikes it.
Eagle-Eyed (Ex)
Requires: None
Effect: Your Ranged Precision ability triples the range increment of your weapon.
Improved Sniping (Ex)
Requires: None
Effect: When you attempt the Sniping option during Stealth, decrease the penalty to -5.
Swift Stealth (Ex)
Requires: None
Effect: You may move up to your full speed when attempting stealth. You can attempt
stealth while running, but you take a -10 penalty to your attempt.
The Quick and the Dead (Su)
Requires: None
Effect: You may draw and reload your weapon as a free action, regardless of the time it
would normally take to do so.
Additionally, during the first round of combat, you inflict maximum damage against any
opponent who has not yet acted.
Ranged Maneuver
Requires: Dexterity 16+; Sniper Shot 1d8
Effect: When you hit your Mark, you may sacrifice 1 Sniper Shot die to initiate a bull rush,
disarm or trip against your opponent, as if you were in an adjacent square. Use your
Dexterity in place of Strength for the purpose of resolving this maneuver.
Cover Fire
Requires: Base Attack +6
Effect: As a full action you may designate a 10 foot radius within your first range
increment as cover fire zone. Allies within this radius have Partial Cover, and enemies
treat this radius as difficult terrain.
Improved Cover Fire
Requires: Cover Fire
Effect: When you use cover fire, allies within a 15 foot radius are treated as having
standard cover. Enemies treat every square of movement as 3 squares.
Thrown Weapon Mastery
Requires: None
Effect: Thrown weapons you employ inflict damage as if they were one size category
larger. You never suffer penalties for using improvised thrown weapons.
True Sniper
Requires: Sniper level 9
Effect: You automatically confirm any critical you threaten while wielding a ranged
weapon.
Anyway, hope this helps of offers some inspiration!