Hm, my top 3... my top 3... arrrgh, sorry, can't choose only 3 to be my top games over all those years...
- Hexuma is one I played so many times, that I knew it by heart
- DSA 1 - die Schicksalsklinge (don't know, if the game was released in other languages)
I played it over all the years, last time I played it was last year
- Hero (on an old atari 400- console, I ever wondered, why this wasn't made for real computers later, I loved to fly with this fellow through the lava-levels)
- all Quest for Glory-titles, Eye of the Beholder series and of course the Ultima-series (except the 9th, that I have missed somehow), oh and sure the good old Monkey Island :)
and...and...and...

it annoyed me to NO end that one of the only ways to get "hurt" in below the root was by bumping into walls.
i've bumped into many walls and have never been hurt by one of them.
i remember being quite indignant about this as a child while playing it on the c-64.

Classics:
1. Sid Meier's Alpha Centauri
2. Full Throttle
3. Tie Fighter

1) Deus Ex
2) Victoria: An Empire under the Sun
3) American Mcgee's Alice
Pathologic surely wins the special price for the most underrated game of all times.

falcon 4.0 with ether red viper or openfalcon mod
stalker shadow of chernobyl AMK mod
ArmA combat operations/armed assault

In no particular order as its just too heartbreaking to pick lol :
Monkey Island II
Street Fighter II Turbo
Punch Out
I must give an honorable mention also to :
Ghostbusters on the Spectrum and Mega Man
:D

1.) Portal
2.) Half Life 2
3.)Fire Emblem (7 in Japan)

Well if it's okay to mention other systems then I'd have to say:
Doom
Flashback
Metroid

1) The Neverhood
2) Quake
3) Commander Keen
The Neverhood was a brilliant and fun claymation game. Created by Doug TenNapel the guy who made Earthworm Jim among others. I hope it comes on here for others to enjoy.
Quake one was a brilliant game. Dark HP Lovecraft style horror and ground breaking 3d. I wasted many hours playing this.
Commander Keen is my favorite platformer, espeically 4-6. They all had great gameplay.

Deus Ex
STALKER
Freespace 2

Hard, really hard, but I guess it's:
1) Duke Nukem 3D
2) Baldur's Gate II
3) Dune II

To all the people mentioning Valve games like Half Life 1 and 2 and Portal, etc. - have you not heard of Valve's Steam? There is no way any Valve title is going to be made available for download from anywhere but Steam!
Let's not get too carried away, eh?! :)

My top 3:
System Shock (1 & 2): SHODAN can take HAL9000 and convert it in a colecovision...
IL-2 Sturmovik: simply put, the best WWII simulator of all times...
Tie Fighter: A rebellion of hippies with a stupid kid, an histeric princess and a pirate as leaders? No way! Glory to the Empire!

Tough choice, but i spose in no order:
Portal
Legend of Zelda: Orcarina of Time
Goldeneye
Need to mention Team Fortress 2 and Smash Bros. Melee for being the best multiplayer games ever (behind goldeneye).