Games with extensive hacking scenes... so yeah probably all the games with game specific hacking tools and/or info. I would not have particularly held the NSMB stuff in high regard but hey
Are you more interested in playing hacks or making hacks? For playing then read on, for making then though a community is nice you can do an awful lot by yourself with a bit of learning if you want, say you really like Little Red Riding Hood's Zombie BBQ (and why not as it is a great little shooter). You could probably get some level or difficulty mods going pretty easily despite there not being a community surrounding the hacking of it.
Mario 64 DS had something at one point, and still has a decent level viewer/editor. Not sure where it lives these days.
Mario Kart
http://wiki.tockdom.com/wiki/Main_Page
Advance Wars
http://forums.warsworldnews.com/index.php
Golden Sun (though it might be more for the GBA)
http://forum.goldensunhacking.net/
Fire Emblem
http://www.feshrine.net/
http://serenesforest.net/
Pokemon, this would be the big one. I am not sure of the current sites that house most things.
http://www.pokecommunity.com/forumdisplay.php?f=156 is probably still the biggest here.
http://bulbapedia.bulbagarden.net/wiki/ROM_hacks is also worth a read and there are loads of little sites (
http://projectpokemon.org/wiki/Main_Page for example).
A lot of the bigger projects and people within the scenes will also have an account here as well.
There are also tools for specific games, things like
https://github.com/nickworonekin/puyotools for puyo puyo, phoenix wright has a few things and if you want to actually hack a popular franchise (megaman*, final fantasy*, inazuma 11 and such like) or popular games then a there is probably someone the know what goes (though in most cases you can probably make a thread and find someone that knows or just pulls apart the game to have a look). You will probably not find so many hacks that you can play with in those sorts of games though. Equally I should link up
http://www.insanedifficulty.com/board/index.php?/files/ as it is good.
I might as well also say that despite it being for the GBA then fire pro wrestling has a surprisingly solid community for hacking it.
*go back to the SNES and the communities/tools for hacking these games, to say nothing of the amount of hacks for them, are quite big, they do not seem to be as active for the GBA and DS side of things though. Not absent but not much beyond translation has been done.