Baldur's Gate, Baldur's Gate II, Icewind Dale, Icewind Dale II, and Planescape: Torment - all on disc and GOG.
Half-Life and its addons - in an old-school cardboard box (Half-Life Anthology or something), then again in a DVD case because I'd lost the discs and the key(s) from the first copy wouldn't register on Steam so I had no way to play them.
Saints Row 2 - for Windows and X-Box 360
Anomaly: Warzone Earth - Humble (Bundle) and GOG
Darwinia - ordered a CD (and a poster) directly from Introversion, then bought it again from GOG
Icewind Dale, - got it in a Humble Bundle and thought it was much too good for that price so I bought it again from GOG, then it was included in one or two other bundles but those don't add more copies, just more money paid for that one copy.
Dust: An Elysian Tale - again, bundle, then GOG because it's that good.
Ground Control - disc, then GOG
Homeworld II - twice on disc from promo bins, second time because I forgot I had it already
The Longest Journey - Swedish-language version (Den Längsta Resan) in an old-school cardboard box, then English-language on GOG.
Myst, Riven, and Myst V - first in DVD-style cases then on GOG, I also already had two disc-only copies of Myst for Mac that were given to me by people who got them bundled with their Mac.
Myst III: Exile - double DVD case (yes, pretty much two DVD cases glued together, I'm still not sure whether I should instead have bought the similarly-sized cardboard box that was also available - the latter looked much better, but I wouldn't have had this story then to tell), and I later found a Collector's Edition box so I just had to buy that one too.
Uru: Ages Beyond Myst - DVD-sized Collector's Edition cardboard box (didn't have any expansions yet), then GOG.
There are most likely many others, but these are ones that I remember after a quick look among my discs and GOG collection.
Post edited January 22, 2015 by Maighstir