EmuParadise.me - A giant collection of emulators and roms. One of the best!

CoolRom - A Rom collection with only working dumps. Great for quickly finding known roms.

ROM Collector - A cool site where you can purchase ROM sets on CD for a nominal fee, mailed directly to you. Very cool for the avid collectors out there.

GameBoy Advance ROMs - This site specializes in GBA ROMs. They have anything and everything related to GameBoy Advance.

ROMNation - Probably the 2nd most comprehensive, easy to use, BIG romsite on the 'net. Thousands and thousands of games for dozens of popular systems. Top-notch quality emulation.

TheROMs.com - Thousands of ROMs, hundreds of emulators, zero BS.

RomCenter - Audit and repair your roms with this program. Site also hosts hundreds of games available for download.