Gah, throughout the course of the 20 years Zelda has been around, there's been so many great songs that it's hard to single out any one of them. But, I do have a couple favorites that are definitely the best in the whole series in my opinion.
MM - Song of Healing: I can't even explain this one. It just seems...... powerful, if you know what I mean. Like it sets the perfect mood for the entire game
ALttP - The Hyrule Castle Theme: I loved this one. Easily one of my favorites in ALttP. Too bad they ruined it in WW though. I always thought it should be a sinister theme, reflecting true evil. WW made it into some kind of sad slow tune...... It was great to see it back in TP as a truly sinister tune.
OoT/TP - Song of Time: This one really fits the mood of the Temple of Time. It really makes you feel like you've stepped onto sacred ground, and that this place holds something very special. Definitely memorable.
Those are three of them, but I'm sure I like some better that I forgot to mention them here. Like I said, each game had some excellent songs, and it all adds up to a huge amount that's hard to remember.