Ocarina of Time is my favorite Zelda game as well as my favorite game. I play through it once or twice every year and still have a lot of fun with it. Zelda II and Link to the Past follow closely behind on my list. While Zelda is my favorite series I have to agree with Karyann on Phantom Hourglass and Spirit Tracks, did not enjoy those games at all. I still have not finished all of the games yet though, so I might eventually have a new favorite, but I doubt it.
Finished: LoZ, AoL, ALttP, OoT, FS, FSA, TMC, TP, ST, SS, ALBW
Played: LA, MM, OoS, TWW, PH
Never Played: OoA,