Let me throw my 2 cents:
Personally, I prefer Wind Waker over Twilight Princess.
I loved being able to set sail towards the unknown and finding islands, treasure, maps and other secrets as I explored The Great Sea. Whenever I tried doing that in Twilight Princess (mount Epona and explore Hyrule) I could barely find anything, whereas in Wind Waker there was at least one hidden treasure or a side-quest in nearly every island.
Twilight was rather weak in the side-quest department. The only rewards for Soul Hunting and Bug Catching were things connected with money, I believe (correct me if I'm wrong). The rest of the side-quests in that game were mini-games and that monster-filled cave in the desert.
In Wind waker, there were tons of little side-quests (Ex.: The Auction, the Koroks, the Giant Pig, Moe the moblin, etc.) that had worthy prizes and rewards like heart pieces and charts. Plus, the Figurine Gallery was awesome, even if there wasn't anything worth the trouble (other than the feeling of acomplishment).
With all these side-quests, Wind Waker felt like a complete world, even if there were only two or three towns in the game.
Twilight Princess felt like a barren world. There were also two or three towns in the game, but they weren't as active as the ones in Wind Waker.
Wind Waker was also better in the music and sound department. There were a lot of memorable tunes in Wind Waker.
In Twilight Princess, the music isn't memorable, but that is because its function is to give you the feeling that you're actually in those locations (Hope you know what I'm trying to say). The same thing happened in Metroid Prime. Still, there were a few memorable tunes in TP, mainly the Boss Themes.
Graphics-wise, I prefer an artistically beautiful game to one that has realistic visuals. Even if I love the character and monster design in both games, I love the art style in Wind Waker more.
In the Gameplay department, I must admit that the Twilight Princess items and battle system were better and more fun to use. I loved the battle techniques, as well as the "BeyBlade" and the Ball & Chain (even if there weren't many uses for them in the open field). I also thought that the Dungeons and Boss fights were better thought out than in Wind Waker. The Arbiter Grounds Boss remains as one of my All-Time favorites.
Twilight Princess was also longer than Wind Waker, but it felt shorter, since there was little to do besides the main quest.
Finally, Wind Waker's story was better explained and managed to hook me. Twilight Princess, not so much. (Plus, I prefer WW's Ganondorf over the TP one)
Conclusion:
Wind Waker had the best overall game while Twilight Princess had the best main game (without side-quests).
Phew, this post turned out waaaay longer than expected.