The Game Libratory, at UC San Diego
Atari Games from the Collection
NOTCOT did a great sneak-peak of our home at UCSD, in the Center for Research in Computers in the Arts (CRCA): the Game Libratory!
“The Game Libratory is a new game library / laboratory whose mission is to provide researchers with access to game hardware and software.”
At the Game Libratory we’ve got nearly every game platform from the PS3 to the Atari2600, and literally hundreds of pounds of games. There are still gaping holes, however, so donations are welcome! 
Unfortunately, I’m not aware of any institutions that are archiving legacy hardware and software. To guide our R&D for the TV-Computer, we are hoping to find an archive of educational games, for the Apple II and other early systems.