Finally got around to this. Feel free to transplant into OP. @Peltz
The only improvements would be to add links within the OP for all the platforms that are in there. Until then a bunch of these just point to the top of the OP.
Multi platform
Floppy disks
INLretro Dumper-Programmer (kazzo)
No-Intro, guides
Redump, guides
Retrode
Retron5
Specific platforms
2600
C64
Colecovision Flashback
Dreamcast
DSiWare, transfer from CFW 3DS to CFW DSi
GB/GBC, using Everdrive 64
FDS
N64
NDS, using CFW 3DS
NDS, using CFW DSi
NDS, using dongle
NDS, using flash cart
NES
NGC, using Wii
PCE/TG16
PCE CD
PlayStation Classic
PlayStation 1/2
Saturn/SegaCD
SNES, using SuperNT
Wii
Wii VC
WiiWare
Specific games (bundled ROMs)
Disney Afternoon Collection
Megaman Legacy Collection
MaBoShi, NDS ROM from WiiWare game
Sonic Adventure DX
Street Fighter 30th Anniversary
Various Wii games