I bought Oblivion 3 times, retail PC (the disk broke), 360 version and Steam.
Company of Heroes twice, one retail (damned disk broke too) and another on Steam, including expansions.
Fear twice, one retail (shitty spanish version) and another on Steam.
Far Cry twice, retail (shitty spanish version) and Steam.
Call of Duty 4 twice, one retail and another on Steam.
Doom 3 twice, retail and the id Super Pack through Steam.
BioShock twice, PC retail and 360 version.
Super Meat Boy twice, one at a discount through Steam and another in a Humble Indie Bundle.
Amnesia, same as with SMB.
Penumbra Overture like 3 times, 2 Humble Indie Bundles and another through Frictional themselves, with included Black Plague and Requiem. I bought them through Steam too, just for the lulz.
I bought Guild Wars twice (thrice if you count a gift I gave to a friend through a Steam sale), I bought the vanilla GOTY edition and the Trilogy edition, not counting the Eye of The North expansion, all of them retail.
Also, I've bought World of Goo like 4 or 5 times, including Bundles. I've honestly lost the count.
And that's all I can remember for now.