Having never finished LttP, OoT or WW, I was really just blown away by TP, and it's the only one I completed. The dungoens and puzzles were quite clever and fun, but I will admit that the last dungeon and the final boss battles were more of a chore than a pleasure. Still, TP is up there with FFIII as far as RPG experiences go.
Incidentally, I started playing WW again after I beat TP, and I was disappointed with the controls and the sailing -- ugh -- the sailing was a HUGE turn off.
BTW, when I restarted WW, I was surprised to find out that I had quit in the middle of the FIRST dungeon.