Here are my top 3:
1. One Piece (The story keeps getting better and better. If you watch this and you're not reading the manga, you really should)
2. Hajime No Ippo ( Somehow this anime, which should be boring and repetitive, stayed interesting throughout. The manga on the other hand, is really getting annoying. It feels like it is going nowhere)
3. Code Geass (It has the best elements of the Gundam series and Deathnote put together. The ending is also perfect IMO)
Other anime that I really like but in no particular order:
Naruto, Bleach, Rurouni Kenshin, Yu Yu Hakusho, Gundam 00, Dragonball, Deathnote, History's Strongest Disciple: Kenichi, Full Metal Panic (mostly for its comedy),
and "Samurai Champloo" as an honorable mention because it had the funniest episode I've ever seen. The episode titled, Baseball Blues, had me laughing my ass off. I can't remember any other time where I laughed that hard from an anime.
