Here it is, all by file name;

8-6-09
kfm
weregaruru
Link
Cloud_S
orochi
JShomer
peter
cell
iori yagami = ihoo1836
zerosvc
VENOM
Spiderman
evilryuMB*
vegetaub22
KY_GGX
AXL
warakia
SonicV2
Adrenaline
seph
sspiderman
carnage
SuperMari o
kfg
DragonClaw
Dcat_Axel
Dcat_Sketch
dracula
snake
master chief
mastrhnd
GhostRider
spawn
BATMANJLA
joker
Static
Broli_Nightmare
MajinBuu2005
vegeta
CvSIchigo
shadow
abyss
kingbehinnmot h*
kira
god_orochi
DukeNukemv1
Black_heart
Rorschach

Now, for the heck of it, here's a couple of the bonus stages I've found;

StrengthTraining
Catwalk
DuckHunt
SkyChase

Added 8-7-09
Cammy
Dan
Guy
Honda
Morrigan
Ryu
Sakura
ShinGouki
Vega
CVS_Kyo

Added 8-8-09 to 8-9-09
MVC2_Amingo
MVC2_Cable
capamerica
MVC2_Hulk
juggy
MVC2_Magneto
MVC2_Omega_Red
MVC2_Wolverine
Punisher
sabre
ironman
thor
G alactus
symbioteonslaught
hulk2099*

Added 8-11-09
norris (yes, THE norris. Still trying to beat him though...)

*Deleted

I'll be updating it every now and then when I get someone new. Till then, this is all I got!