Counting down
5 - Tropico
4 - The Witcher 2
3 - System Shock 2
2 - Giants: Citizen Kabuto
1 - Deus Ex

Honorable mentions that were really, really close but had to be cut (no order) - King's Quest VI, Evil Genius, Medal of Honor: Allied Assault

1. Gabriel Knight : Sins of the Fathers
2. The Beast Within
3. Baldur's Gate 2
4. Lands of Lore
4. World of Xeen (in the Might and Magic 6 pack)

I haven't played nearly all to make a decision, but I am pretty sure some of the following games could make it to the top 5 GOG games:

Far Cry 2 (this would definitely make it, I enjoyed it quite a bit and will probably replay it at some point)
Some of the Prince of Persia games, maybe even all four.
The Witcher 1-2
Driver: Parallel Lines (the little I've played it, I liked so far)

BTW, I recall someone saying that Far Cry 2 is like a poor man's STALKER. Maybe that gave me too high hopes for STALKER, as for some reason I didn't enjoy it much the little I've played so far. But I've barely scratched its surface, maybe I'll enjoy STALKER more later.