I have 4 copies of GTAIV: 2 in part to black friday sales
3 copies of Bioshock: one on each platform
Peggle: iphone, PSN, PC
Metal gear solid 1: 3 copies
mgs2: 2 copies
mgs3: 3 copies
Braid: PC, PSN (due to 1/2 off sale dammit!), xbla
There are many more I'm sure these come directly to mind though,
Two more FFXII x3 : LE, International, Regular
FFVII x 4: PSN release, A green label copy, a black label copy, and last but not least a PC copy (the original not the EA classics one with the gold trim)
Controllers: 2 dual shocks, 2 sixaxis, rb1 strat, rb2 strat, GHWTar, rb2 drums, DJ turntable, the chatpad thingy, the bluetooth remote, and My Harmony One with the PS3 addon dongle.