Majora's Mask never gets the love it deserves. I have trouble deciding which is my favorite. My tops are OoT, MM, Zelda 1, and LA. The Nintendo ones trump all of the CapCom ones, IMHO.
The Oracles are good, but LA is definitely my favorite handheld one, Zelda 1 is my favorite 2D console one and it's a definite tie between OoT and MM for 3D. They are just so different I have trouble picking between OoT and MM.
I love how dark MM is, but OoT just really kept that LoZ feel with the expansive, open environment. I honestly can't think of a LoZ that I haven't enjoyed. I even loved most of WW. I didn't enjoy the Triforce Quest, but I really appreciate the concept of it. They tried to give a real throw back to Zelda 1 with a fully open, non-linear, unbelievably huge environment. Fantastic idea, poorly executed.
EDIT: BTW, I own most of the Zeldas, just not Zelda 2, Four Swords and Minish cap, though I have played through all of them since the ones I don't own, my best friend does. And the series absolutely follows a timeline and anyone who can't accept that really hasn't paid any attention. There are more than enough context clues to piece together a timeline and it has already been revealed that there IS a timeline. It is a split timeline. It starts with Minish Cap and Four Swords then OoT is where the split happens. One timeline where Ganondorf has taken power and been defeated by Link and another where that has yet to happen. All Zelda games are created completely disregarding the timeline and then fit into the timeline after development is complete so it does not affect the game itself.