Twilight Princess is the better game in my opinion.
I just love everything about it! The graphics are really appealing, the music is absolutely amazing, Midna is a great character with a good story behind her, the temples are really good, etc etc etc...I could go on forever, really!
But Wind Waker... Ehh, I don't really care for it... It's infact my least favourite game.
I don't like the whole idea of Hyrule being flooded... I don't like the whole sailing thing, very boring... And the graphics, not my style...
So yeah, TP definitely wins this for me!