I'm looking for the best animal...

[atemu1234]

It has to be small, medium, or large, needs a lot of hit dice, good abilities, etc...

[Kevingway]

I like the Phynxkin from Races of the Dragon. Get some draconic flavor in your animal.

[Phelix-Mu]

Um, pound-for-pound, it's hard to get sillier than fleshraker. Leaping Pounce or whatever it is is a very silly ability, allowing the thing to leap, pounce, and pin a creature in a pretty fast combo. If you advance one up to large, it becomes a real terror.

But there are some other pretty good animals, too. If you could be a little more specific about what you are seeking or the purpose to which the animal is being put, then that would be most helpful in narrowing down the usual suspects.

[LTwerewolf]

What you want it for matters, then we could give you better answers.

[atemu1234]

What you want it for matters, then we could give you better answers.

Lycanthrope for an NPC.

[dhdydg]

At low levels, riding dogs come with useful Druid companions.

[Pilo]

I like the climbdog (Arms and Equipment Guide) better than the riding dog.

[eggynack]

I like the climbdog (Arms and Equipment Guide) better than the riding dog.
That lack of tripping ability is a serious downside. Probably more important than the climbdog's marginally better stats and climbing ability.

[Bronk]

It has to be small, medium, or large, needs a lot of hit dice, good abilities, etc...

I like the tiger... Large, 6HD, but up to 12HD before tipping over into huge (which makes it more powerful than a dire tiger). Three improved natural attacks, plus pounce, rakes, improved grab and scent make tigers pretty powerful animals.

[lytokk]

Lycanthrope for an NPC.

As pointed out, fleshraker would make a pretty decent animal, and I think at least an average lycanthropic form. Of course, the character is going to have to eat the 4 levels in animal HD in addition to the +2 LA if he's afflicted, unless you use the buyoff rules.

I made a were-eagle not too long ago. If you're interested I could share the stats.

[LTwerewolf]

Phynxkin is imo one of the best lycanthrope options out there. 2RHD, and your LA, but you're getting a super easy source of pounce.

[Urpriest]

For Lycanthropy, if you need to stick with a Medium NPC, definitely check out the legendaries. Legendary Tiger has a good deal of oomph for a Large creature.

[Hurnn]

I like the bears, black is a bit lack luster but brown and dire while not great at any one thing are good at nearly everything.

[Fizban]

Brown Bear. It's really, really hard to beat the Brown Bear's 27 strength. If you want charging, there's Tiger, Megaraptor (errata reduced it from huge to large, check d20srd), or Rhinocerous (or Cave Triceratops from Mini's Handbook if you want to get cute).

But wait! You thought Dire animals were actually bigger? Nope, not always: Dire Bear, Dire Tiger, both still only large size. You really can't beat those, a Druid might switch to plants or elementals for wild shape at large size later on but sticking with animals the Dire Bear/Tiger is the best you can get for large.

However, if you want the actual strongest animal you're gonna have to go bigger. The best animal at Huge size, suitable for say an ogre or troll lycanthrope? Dire Polar Bear, Frostburn. Sure the Allosaurus (MMII) has rake and trample, and the Ceratosaurus (Serpent Kingdoms) has a sweet rend I call the "double bite", but only the Tyranosaurus has the hp to match the DPB-and with only one bite attack it cannot match the raw full attack damage of a Dire Polar Bear in a clash of titans.

I think gargantuan is a bit silly but for completion's sake: MMII has Dire Elephant and Spinosaurus, or Seismosaurus for Colossal. The first two will beat the DPB as one would expect, and the Seismosaur will just trample until everything's gone even though it only has one attack, but they're too big to be useful.