ブックオフ "Book Off" A little more pricey than Media Land but still cheaper than anywhere else. Said to be the best place for consoles 500-1,000 Yen cheaper than any of the competition.
メディアランド "Media Land" Definitely the best place for games both new and used in Akihabara.
Hope this helps. Best of luck and welcome to Acid Mods! I hope you enjoy your stay! Check out some more of the forums.
-TwisT