I haven't even started Wario Land 4, Minish Cap, Fire Emblem or Metroid yet. Currently I think my favorite is F-Zero (this would be my first time playing the series).

All the GBA ones.

Pretty much this. The NES games don't really tickle my fancy, except for maybe Super Mario Bros.

Tie between Yoshi's Island, MKSC, and FE:SS. I have respect for the NES games, but have more fun with the GBA games.

I'm tied up between Metroid Fusion and Fire Emblem Sacred Stones at the moment, I'll come back with an answer later

Out of the GBA games... It's a hard choice. They're all so incredibly good. Metroid Fusion is what I'm currently blasting through, with a little bit of WarioWare and Mario Vs. DK on the side. Christmas came early, it seems.

I haven't played all of them for very long, yet, but I'm pretty sure Fire Emblem takes the top. It's my first in the series (I've wanted to try the series before, but I wasn't completely sure), I and I am loving it so far. It really makes me want to try out some more Fire Emblem games, which I plan on doing. But, honestly, I like them all, but like I said, Fire Emblem is probably the best.

Honorable Mentions:
WarioWare, Inc. : Mega Microgames
The Legend of Zelda: Minish Cap
Mario vs. Donkey Kong

Out of the ones I've played so far, Warioware Inc. Mega Microgames. I love it. I'm sure my answer will change once I play the remaining games.

Wario Ware is my favorite. I've always loved these games. Wario Land 4 comes in a close second, though.

Fire Emblem would be my favorite. (I was unaware characters die forever, so I screwed up pretty early, fml)

Out of the ones I've played so far, Yoshi's Island or Wario Land 4 is my favorite. I've only played a few of the NES games and the first five GBA games though.

Well, now that we have the GBA games, I'm going to vote Zelda Minish Cap as my favorite, but people who know me around these parts won't be shocked by that. (lol) Playing it now and loving it to bits.

F - Zero, Metroid and Wario Land 4 are my favourtites so far. But I wish they had of given us a proper Mario game as well.

@ billy-beauts
Yoshi's Island isn't enough of a Mario game for you?
After all it's called super Mario world 2 and Bowser is even in it.
You could also give Mario Vs DK a try.

@ Link79 I'm not really into the whole chucking eggs stuff. I just want to run, jump, stomp and power up basically. I've tried Mario Vs DK and it reminds me do DK'94, so I should enjoy it to some extent. Thanks. What's your favourite?

The gba version of Yoshi's Island seems to take a hit in the sound quality and I don't seem to prefer the added voices, but the game still stays the same and still hold it above the rest. But I still enjoy them, particularly Warioware and Metroid.

My favorite is probably Kirby and the amazing mirror. It's one of the games I never got to try. Most of these ambassador games I already played years ago but they're all great. Mario VS DK is new to me and I never tried any Warioware games. Not sure what to think of that yet.

I never played most of these until now.. My ultimate fave is Minish Cap, of course I do quite enjoy Kirby Amazing Mirror, as addicting as Kirby's Adventure! I am so in love with Mario Vs. DK (great game!!) I played the DsiWare Minis March Again and Gameboy Donkey Kong (94) recently and I see how the games inspire each other. Phenomenal! Also, I am currently in love with Mega Microgame$. I had it when it first came out and forgot about it all these years later. The mini games are so great! i'm also enjoying Yoshi's Island. Oh man. And Metroid Fusion! Another great one. I'm just loving them all, it seems. My least favorite is Fire Emblem. I got bored within 3 minutes of playing it.

Back when I had a GameBoy Advance, I might have well just called it PokemonBoy Advance because that was the only game I played on it. So, despite some dabbling these games are all new to me. I like about half of them, which I think is normal.

1) Minish Cap
2) Yoshi's Island
3) Metroid: Fusion
4) Kirby: Amazing Mirror

My top 4. Cant rate the others yet as I havent tried them out or played them before.