OoT had the story, cast, and pacing. Even the dungeons are fun to replay; I can't say that for any other LoZ.
MM had the scenery, bosses, and combat upgrades (plus other enhancing mechanics through the masks and Song of Double/Half Time, Bomber's Notebook, Time-Traveling Banker Girl with ADD, etc.).
TP had the collectible items (Bugs, Poes, Heart Pieces), graphics, and control mechanics on the Wii version.
The best LoZ game would combine these.
Overall, though, I probably would have to say OoT is the best overall from what I've played recently. The pacing is just infinitely better than MM and TP. The control mechanics are clunky at best, though, and the bosses are a sheer waiting game. Not hard, though they'll kill you if you get impatient having to wait out their attacks.