web resources

Sites that Emulate/Archive Old Web Sites
Spacehey
Webneko
Archive.org

Video Game Sprites and Resources
Videogamesprites.net
Spriters Resource
Snes Maps
Open Game Art

Video Game Music Downloads
Khinsider
VGM Halley's Comet Software

Roms/Emulator Related Sites
Here i only recommend emulators that I have used and think positively of, so I am a bit particular about what I add to this list!
Vimm's Lair
Mother 3 Fan Translation
H Shop (3DS Games)
Flashpoint - old flash games
New Super Ultimate Injector 3DS - use this to create virtual console roms for hacked 3DS'
Snes9x - Super Nintendo Emulator
VisualBoyAdvance - GameBoy Advance Emulator
Dolphin Emulator - Gamecube/Wii Emulator
DeSmuME - DS Emulator
Emulator Zone - list of emulators for most consoles. can't attest to the quality of all on here but it may be helpful
3DS Theme Editor