My favorite would either be Spirit Tracks, or the original! I like spirit tracks because of the fun gameplay elements added, but I really like the original because of how open it is. Not until I found Zelda Dungeon did I find out about the moblin hideouts (not to mention i played the whole thing out of order the first time.)
i never was able to play this when it came out. for some reason i passed it by like many GBA games. however now that i have it on my 3DS being an ambassador, i love it. the graphics still hold up and it is addictive as ever. i have yet to finish but if the beginning is any indication this may turn out to be my favorite 2D game.
Minish Cap is an excellent 2D Zelda title, I really really enjoyed it, especially as I'd completed WW not too long before I played MC for the 1st time, I was shocked to see that they had managed to convey so much of what made WW a great game into something so small as a GBA cartridge! Amazing!!!
I still think ALtTP is my faveourite Handheld 2D Zelda game though
I just started playing Minish Cap for the first time this weekend, and I'm loving it. I'd say so far it's my favorite "originally on a handheld Zelda" which means it overtakes Link's Awakening IMO. Among the 2d Zeldas I like LoZ and ALTTP more though.
The Minish Cap - Worst 2D Zelda, at least the European version. All glitches from the original GBA version are still present on the 3DS (like missing bomb bag upgrade). That's really bad, Nintendo!
I've only played a little bit of MC for the first time but as of now I'm enjoying so far. It stinks that I have to spend my vacation doing homework and studying, plus my Christmas presents so I don't think I'm going to focus on the game in a while.
I would say OoX are the best 2D Zeldas. They have a lot about them that I truly enjoyed, whereas MC just had nice combat (imo). I loved the OoX story, it made a bit more sense in my eyes as well.
The Oracles are good, and Link's Awakening was the first game I ever played, but I'd have to say that The Minish Cap is my favorite handheld 2D Zelda. As for topping the first 3 games, I would still say that Minish Cap is better.