...there was no Punchout on GBA...
Not the same, but there was Hajime no Ippo game on GBA:
...online games on 3DS...
Tekken on 3DS is VERY sensitive to region. If your partner is too far away from you, it will be lagfest and it will be like you are submerged into a bowl of honey.
Dead of Alive Dimensions lobbies were dead last time i checked few years ago, so i couldn't find a game.
Street Fighter IV is really good, the only problem is that if you allow touchscreen commands, players can spam charge moves (like Guile's sonic boom) constantly. Check the setting before initiating search.
SFIV is also the only game that allows you to play the game while it looks for opponent, you can even progress through singleplayer arcade mode though you most likely won't be able to finish a round because there are plenty of players.
Resident Evil: Revelaitons and Mercenaries have online Raid modes.
Kid Icarus has online multiplayer. And playing it on the bed is actually the best option because you can put it on your lap/belly.