Well for me i personally own more than half of the gog.com games but non-gog version of them i used to have them before..right now i liked the Pure Pinball 2 REDUX the most..astonishing depth of view and graphics in this renewed version

Beneath a Steel Sky or UT2k4.

Out of games sold on gog, that I actually bought from gog, I'd have to say Simon 1 and 2. They bring back so many memories from when I played those on the Amiga.

Redneck Rampage. Don't know why.

I've played 3 games now from GOG: Fallout 1, Fallout 2, and Beneath a Steel Sky.
I'd have to say the best so far was Fallout 1.

Broken Sword 2, the best game on gog until they put up broken sword 1...

Sacred Gold for me.

Patrician 3.
Must. Sell. More. Iron. Goods!

Has to be Feeble Files, Simon games, and Beneath A Steel Sky. You just can't beat a good adventure. ( :

I like several that I purchased (not all I have purchased, but several).
Port Royale 2, Gothic, Stone Keep, Sacred Gold
That is only a somewhat order of how I like them as it depends on the day and what I feel like playing.
Honorable Mentions: Giants, Feeble Files, Soldiers, Beneath a Steel Sky

System Shock 2. Damn I need this game. :P

OPF or Toca 3

Sacrifice
and
Giants: Citizen Kabuto

Sacrifice (even though I had it already in a limited edition boxed version), MDK and MDK2. Oh, Giants gets a mention for the British humor.

Freespace 1 and 2