I'm going to break with the consensus here and give my honest feelings about OoT.
(puts on flame-retardant outerwear)
OoT was not that great. This is coming from a Zelda fan from the time I was 6. I had even saved my allowance/birthday money/etc and pre-ordered OoT months in advance because Gamestop (then called Babbage's) had a tie in for a gold cartridge and Link t-shirt. The first half of the game was pretty good, but I feel like it kind of fell apart around the Kakariko Well. I understand that the game was a "milestone" or whatever, but I felt very let down by the latter part of the game, especially the final battle. The puzzles were too easy and the kill-item system with the bosses did a lot to remove the challenge of defeating them.
TP on the other hand, was something else entirely. This was the game that OoT was supposed to be had the N64 possessed the capability of running it. The character design was better in that the characters were more believable while at the same time, allowing for the comic relief that Nintendo titles possess. While the kill-item concept was still present, it was not as blatantly overpowered as in OoT and some of the bosses actually gave me a bit of difficulty. The puzzles were the aspect of the game that gave me the most trouble and got me stuck on pretty much every occasion, forcing me to brainstorm to try and solve them different ways. If this isn't enough of a reason why I prefer TP over OoT, I'll go ahead and say that I haven't had a game give me the sort of feeling I got from TP since I first played Final Fantasy Tactics.
This having been said, I definitely feel that TP is the best entry in the franchise from a developmental standpoint. On the subject of favorite Zelda title based on Nostalgia, that's a toss-up between Adventure of Link and A Link to the Past. A Link to the Past was awesome because it took the first game in the franchise and re-imagined it much like I feel TP did with OoT, but there was something that was just... missing.
Adventure of Link was just incredible. I enjoy that game so much I have it on both the NES and GBA so I can take it with me.