After receiving my Zelda bonus disk on Friday, and playing through OOT again, then playing through and beating MM for the first time, I will give my 2 cents.
Ocarina of Time was one of the greatest ever made in 1998. Still is today. Ocarina of Time is arguably best Zelda ever, and best ever. I can find almost no faults, and will forever be cherished as a classic. However, LTTP is also my number 1 Zelda ever, and favorite of all time (along with Metroid Prime). I love OOT (the ) even more, especially after it being re-released. All 9 dungeons were SO enjoyable. Inside the Deku Tree, Dodongo's Cavern, Jabu-Jabu's Belly, Forest Temple, Fire Temple, Water Temple, Shadow Temple, Spirit Temple, and Ganon's Tower. From beginning to end a classic. Near perfection.
Majora's Mask had a live up to, from the (IMHO) near-perfect OOT and LTTP. It didn't quite live up to either, but is still a near-classic and is a solid entry into the Zelda series. The lack of dungeons, the foolish focusing on side-quests made it (like tWW) seem rushed. Other than several major and minor flaws, Majora's Mask is worth playing and is one of the best N64 . The three-day system was sheer genius. The four dungeons were all long and engaging- Woodfall Temple, Snowhead Temple, Great Bay Temple, and Stone Tower Temple. The came out and some loved it even more than OOT.