List of stuff that's been taken down

This is sorted by who took the rom down and not who the publisher is. Sometimes the takedown isn't completely thorough, but searching for and listing every discrepancy isn't worth my time.

Nintendo of America

Mario
Zelda
Pokemon (except for Heartgold and SoulSliver)

All the different regions of these franchises were removed

Sega

Sonic
Yakuza
Shin Megami Tensei/Persona

The North American and European versions of these roms have been taken down, but the Japanese roms are still up

Entertainment Software Association

Ace Attorney
Ace Combat
Battlefield
COD
Castlevania
Contra
DMC
Doom
Diablo
Donkey Kong
Dragon Age
Dragon Ball Z
Dragon Warrior/Quest
Elder Scrolls
Fallout
Final Fantasy
Fire Emblem
God of War
Gran Turismo
GTA (except for the Gameboy GTA Games)
inFamous
Jak and Daxter
Just Cause
Kingdom Hearts
Madden
Mass Effect
Max Payne
Medal of Honor
Mega Man
Metal Gear
Metroid
Mortal Kombat
Need For Speed
Pac-Man
Pro Evolution Soccer
Ratchet and Clank
Resident Evil
Soul Calibur
Super Smash Bros
Tales of
Tekken
Splinter Cell
Wolfenstein

Like with Sega, the American and European roms were targeted but the Japanese roms stayed.