I've played every single Zelda, since the first gold cartridge on the NES that I got for my 7th birthday, Link and I are like best buds.
I have to say, Twilight Princess on Wii has been my favorite Zelda thus far. The new tools (especially the double clawshot), the dungeons (arbiter's grounds is amazing), and the new controls (pointing and shooting the bow is just so much better than an analog stick, also, new swordfighting moves).. just made it a "definative" Zelda experience for me. I also liked the horseback combat.
Sure OoT was good too, and prior to TP, it was my favorite Zelda, I'm also a huge fan of A Link to the Past. But TP edged them out, having wolf link gave a little bit of variety to the play, Midna is way less annoying than Navi, the world is bigger for more exploration, and the heart of the game, the dungeons, are better.
Who knows, maybe the next Zelda will trump it. I don't get stuck on game so much and think nothing can top it. Cept Final Fantasy, which hasn't surpassed its peak at VI. But that isn't saying it can't one day surpass VI... it just hasn't happened (yes I know, I opened a can of worms, but hey, I don't care about you VII fans, you go ahead and enjoy your little rewrite of VI's story in futureland with anime heroes and villains, I don't care)
I also don't care if you're going to flame me for not saying OoT was the best. I don't care if it was the first Zelda you ever played so it has this big impact on you. I've been playing the series since it was introduced, and even with that big nostalgia effect, Legend of Zelda (the original NES game) isn't my favorite in the series by a long shot.