Based on Wikipedia...

Madagascar (did not see The Wild)
Antz - liked ABL too, but I enjoyed the Antz storyline more. I personally think it has one of Woody Allen's best performances.
Finding Nemo - Much better than Shark Tale.
Ratatouille - but with a shout-out to Flushed Away. It has it's own charm, and how often do you get to see animated mice voiced by Hugh Jackman and Kate Winslet?
Tie for Shrek/Monsters, Inc. They are both good.
Emperor's New Groove - I agree this is an underrated film. The humor and voice acting is great.

The Wild - Madagascar: I'm not crazy about either to be honest. But the Wild had Eddie Izzard, so... winner!

Antz - Bug's Life: Bug's Life is my favorite of the two, though Antz is a really good movie as well.

Shark Tale - Finding Nemo: even though I think Finding Nemo is slightly overrated, I think it's still miles better than Shark Tale

Flushed Away - Ratatouille: saw both only once a long time ago, so don't know about this one

Shrek - Monsters Inc.: both are fantastic, but I think Monsters Inc. has a slight edge (funnier & more emotional)

The Road to El Dorado - Emperor's New Groove: that's hard. El Dorado's leads were better than Kuzco & Pasha, but the villains were way better in Emperor's New Groove.