I must echo the sentiments here and say that picking three of my all time favorite PC games is hard to do, but...
1. Master of Orion - Probably my favorite turn based 4X strategy game of all time. Played the original to death when I was younger, and I am sad that I don't have a copy of it anymore. MOO2 was good, but I always liked the first one the best. I won't even talk about MOO3 here...
2. X-Com UFO Defense - This game has been able to stand the test of time, and I still dump hours into this game even today.
3. X-Wing/Tie Fighter Series - So you're saying I can fly an X-Wing against the evil Galactic Empire and go on the Death Star trench run? Are you saying that I can fly a TIE Fighter and shoot down Rebel scum? Yes you say, and it's even more awesome than it sounds? Sign me up because X-Wing and TIE Fighter are my two most favorite combat space sims of all time.
Honerable Mention:
1. Civilization series - It was tough not putting this in the top 3, but really, I shouldn't have to say more about this acclaimed series.
2. Wing Commander series - Always loved these games back in the old days.
3. Shogun - Total War - I love every game in this series, but for some reason, I keep going back to Shogun. Too bad that it doesn't play correctly with the Nvidia 8xxx series graphics cards...
4. Freespace 2 - One of the best space combat sims of all time.
... and much, much more!

1. Age of the Empires 2
2. Fable
3. KOTOR

Dungeon Keeper 1 and 2
Baldur's Gate Series
Planescape Torment

In no order:
Fallout 1&2 - because of it's atmosphere and feeling
X-COM: Ufo Defense (aka UFO: Enemy Unknown) - because of it's replayability and complexity
Portal - because of perfect execution of great idea; gameplay, script, style, atmosphere, sound&music, Portal has it all. Every single second of playing redefines meaning of the word "fun".
Aside from this TOP 3, I have to mention Silent Hill 2. It didn't make it there for one only reason - gameplay was quite boring. Everything else was perfect. It was the first (and only) game that made me cry.

I like RPGs... so here are my top 3 favorites:
1. Planescape:Torment (I consider it the best game I played... great storry, awesome caracters, good graphics. In my oppinion you are not a true RPGer if you didn't played PS:T )
2. Fallout series (Fallout 1 was my 1st RPG and it got me "hooked')
3. Baldur's Gate series (I started to replay BG2... I think it is the 21th time I do it and is still fun)
must mention:
4. Neverwinter Nights series
5. Icewind Dale series
6. Diablo series

The games that have enthralled me and absorbed most of my time?
1. Medieval: Total War + Viking Invasion + Patch 2.01
Simply the most amazing strategy game ever made.
The game is awesome, the myriad of mods even more so.
Been playing this game on and off for five plus years now, sunk literally thousands of hours into it.
2. Deus Ex
Simply the most amazing Action RPG ever made.
3. Operation Flashpoint + Expansions + Patches
Simply the most amazing simulation ever made.
4. Thief 2
I'm cheating, i cannot not mention Thief 2 when talking about my favourite all time games.

1) Nethack
I think no one mentioned it yet. For me it is a clear and solid number one. The game I always keep returning to and that still, after 10+ years of more or less regularly playing, it keeps offering something new (even without the updates and add-ons).
2) Civ (or maybe Colonization)
3) X-COM
But oh so many other favourites: Jagged Alliance series, Baldur's Gate 2, Star Craft, Settlers series, NHL 95&96, NHL 2002 demo (don't ask ;-)), lots of C-64 games (and especially Pirates), etc.

It just has to be
1. MTW and Viking Invasion - so many hours spent on this one.
2. X-Com - The first two were fantastic.
3. Baldurs Gate 2 - Its just so big!

1. Civilization 2 - This game made me use my brain so much when i was just 10. Thank YOU!
2. super Mario Bros 3- Different Distinct worlds - minigames and the ability t fly. Best Platformer EVER.
3. ZORK!

Top 3? How about we change the thread title to "Top 30"?
It would be much easier;)
1. "Outcast" (by Infogrames)
I like to think about this game as an example of a reference game scenario.
When it comes to the story - this IS the way games should be designed these days.
If the story is boring, the game can have all the fireworks you want, and it's still going to be crappy :)
2. "System Shock 2" (by Looking Glass)
It made me feel like I was really the last person on earth (in space:)
This game has climate like none other!
3. "Doom 3" (by ID)
First game that actually scared the living hell out of me and almost gave me an heart attack! Picture this - it's 4 a.m. I'm playing with my earphones. I've just runned into the dark room with "something" crawling inside. It's my last few rounds, 10% health, I'm desperatly trying to locate the monster by the creepy sound it makes, and suddenly; BAM! Something REALLY grabs my neck!
It was my father, yelling "Go to sleep, it's 4a.m for God's sake!" (HE actually tought it's going to be very funny:)

1. Fallout
- It made me play 16 hours in one session
2. System Shock
- First game that scared me. Also the voice of SHODAN is unforgettable
3. Wizardry 7
- First "dungeon" type RPG I ever played on computer.

Very hard to choose, but if I had to......
1) Elder Scrolls II - Daggerfall
(Buggy as hell, extremely difficulty and not forgiving to novice players, but I really loved it)
2) Planescape : Torment
(The best RPG of all time?)
3) Starcraft
(Many "acclaimed" strategies that followed "borrowed" ideas from this one, as well as Age of Empires)
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Note : I feel a bit guilty for not including Baldur's Gate I+II, Wing Commander, and many many others...... :(

Total Annihilation
Unreal
Quake

1. Shadow of the Colossus
Probably the most epic game of all time, and the emotional impact this game has on me is unrivalled. Total immersion.
2. The Myst-series
Fantastic atmosphere and design. The feeling you get when you finally figure out a hard puzzle is pretty damn close to the definition of catharsis.
3. This place is reserved for Heavy Rain when it's released. :p

My top 3 games? This'll be tough, but...
1) Wing Commander IV
2) Mafia
3) Grim Fandango