For 3D, it is between MM and Skyward Sword. However, I would say MM had more emotion, so it tops SS. Don't get me wrong. Skyward Sword is an amazing game, but Majora's Mask truly had inspiration behind it, and enough content to keep you busy for hours and hours upon end!
With MM, the characters are living, breathing people who are each catered to within each second of the game's 3 days! There are SO many hidden scenes in that game which make you actually care about them, and actually feel bad about them having to die! One hidden scene which really stuck out in my opinion is if you save Romani from the "ghosts", then on the third day you can view a scene where Cremia plans to get her drunk and sleep with her so that she would not realize as the moon falls and their lives end.
Such thought-provoking scenes like that really makes you care about its characters more! If you pay attention to the details of MM, it really makes you want to save them all! The polish of this game is EXTRAORDINARY!!!
As for 2D, it is between Link to the Past and Oracle of Ages. However, Oracle of Ages wins, and for a number of reasons.
1. Unlike ANY other Zelda game, you ACTIVELY PURSUE the villain, who might I add, is a total baddass! While it is true that Ganon hijacks the secret ending, Veran was able to wreck more havoc than any other 2D Zelda game, and accomplish it all herself! I'm not talking about some asshole who just waits in his lair for you to come. Veran ACTIVELY MANIPULATES the characters of the game in an attempt to stop you!
2. Game balance. I'll take A+B over A+Sword any day! Not only that, but unlike LTTP where your sword is so puny you could never hit things, in Oracle of Ages your sword can slay foes with ease!
Did I mention Roc's Feather?
And the absence of fairies? Don't get me wrong, but fairies make Zelda TOO easy! Of course, in the case of LTTP, they balanced foes pretty horribly because enemies deal TOO much damage unless you get the blue and red tunics! So damage is one of the thing Oracle of Ages really got right in compared to LTTP.
Not to mention that seeds are MUCH more fun than magic powder! And the seed shooter was AWESOME! And unlike OoS where by the time you got the triple slingshot the game was over, you get it right in the THIRD dungeon! Compare with LTTP's arrows, which really feel insignificant and don't have much variety, the seed shooter is helpful in SOOOO many situations! Whether you want to burn foes, flat out hurt em, stun em, or blow em away, the seeds are MUCH better than arrows! (And aren't arrows in LTTP too slow in comparison?)
Oh, and the shield too is better. It's actually a usable item instead able to even push foes, as opposed to LTTP where your shield doesn't block the attacks you actually want it to block.
In fact, items as a whole are MUCH better than in LTTP! You actually had weapons in OoS, whereas your only practical weapons in LTTP were a boring hammer, a hooktshot, and a crappy bow.
Oh, did I mention Rings!?
Oracle of Ages definitely had waaaay more strategy and variety in its equipment than LTTP!
3. Nayru was also a much more interesting heroine than Zelda, because you actually rescue her midway through, and even that isn't enough to stop the villain! Plus she's hotter, and has a better theme song. Don't get me wrong either. I enjoy Zelda too, but the Zelda in LTTTP is not a pirate, archer, OR ninja! In LTTP, Zelda is just a useless pussy who you have to save at turtle rock! BOO HOO! What the hell did she ever do for Link besides get his uncle killed!?
4. Length and content. LTTP was simply dungeon-to-dungeon. It was BORING! Whereas Oracle of Ages actually made you work before you could enter the next dungeon, AND it had so many more optional areas to explore for Rings and other unlockables! Not only that, but the time traveling concept was executed WAAAAY better than the dark world! With dark world, you only needed to go back to the light-world TWICE in the entire game! Whereas with the time traveling feature, you would make an impact in one world, and it would appear in the other!
So my conclusions?
Majora's Mask is better than Skyward Sword because of its characters and world leaving a better emotional impact on the player with all its polishing.
While Oracle of Ages is the best 2D Zelda game due to its MUCH better items than any other 2D Zelda game, and its story and world design.