Just a little fun time waster, I love seeing fellow gamers top games.
Basically, post your top three of games of any era or on any system, why you love them, or discuss your top 3 or other's.
I'd say my top 3 would have to be:
1. Deus Ex (PC) I love this game. It's the best game ever imo - I'm nothing less than a Deus Ex fanatic.
2. KoTOR (XBox) Probably the game I've played the most in my entire life - can't stop loving on it.
3. Pharaoh (PC) Oh boy this game is fun. Establishing, building, managing and extending an ancient Egyptian city - it's awesome.

1: Elite 2: Frontier (Amiga)
2: Dune 2 (Amiga)
3: Dungeon Keeper (Pc)

Hmm... this is really hard... I would say..
1. Fallout
2. Arcanum
3. Deus Ex
But I also could vote Monkey Island 1 and 2 and Indiana Jones and the fate of Atalantis or the last crusade into the top 3. It is not easy to pick the right. :)

uhmm...
1) Monkey Island 1
2) Broken sword 1
2b) Broken sword 2 (we cant take them apart
3) Loom

1: Wasteland (Interplay / Apple IIGS) -- a fantastic RPG from a fantastic company. The godfather of post-apocalyptic RPGs.
2: SEAL Team (EA / PC) -- a pretty darned in-depth first-person simulation of team-level combat in the Mekong Delta during the Vietnam War. Huge, exciting, sometimes brutal -- a great game.
3: The Operational Art of War series (Koger? / PC) -- I've spent hundreds and hundreds of hours playing this series, its customization abilities are unmatched... Steel Panthers runs a close second.

I have been playing computer games for 20+ years, so a Top 3 is really impossible, so i'll do this:
Commodore 64:
1) Elite - The classic that always has to be somewhere in any C64 gamers list
2) Redstorm Rising - The best video game based on book or film, tremendous atmosphere!
3) Koronis Rift - an excellent action adventure that was ahead of it's time and so incredibly addictive!
PC:
Not in any order
The Longest Journey - the best story ever put into a digital format
Darklands - an RPG based on German 15th century beliefs and lifestyles. So much historical research, so much detail, and a game that does not have to end, so I have been playing it for 15 years now!
S.T.A.L.K.E.R - The perfect merging of shooter, RPG Lite, horror and a totally believable world that has not been bettered in any game before or since.
The above lists are unfair, undemocratic and downright not correct, for I really would have to list at least 50 games, without any order, to feel I had told you the games I love and are the greatest games ever. I have already thought of a couple more C64 games i could have put up and 4 or 5 PC games I could have put in my Top 3. I chose three that showed the breadth of genres you can have - that in recent years have shrunk terribly. today, on PC, I would say at least 80% of all PC releases are variations on first and third person shooters. We don't get adventure games, or puzzle games, or real RPG's, or simulations or original ideas more than once every 3 or 4 years. In the 90's we had so many genres and so much innovation that that is why it is seen as the golden years of PC gaming.

Wow - you are my type of gamer - all great games that could have gone in my Top 3 along with the Top 3 already there!

1) Max Payne 1 and 2 (I can have two in here, right?)
Easily my favourite games ever. Ever! They're just classics, and never get old. If you haven't played either, you're lost to me.
2) Operation Flashpoint: Cold War Crisis
Truly a magnificent game. Armed Assault is also brilliant, but OFP is still the best.
3) Company of Heroes
Probably the best RTS ever made. Closely followed by Red Alert 2.
Other games that didn't make the list are Portal, HL2, Call of Duty, Ghost Recon, the Hitman series, and Unreal Tournament '99. Oh, and Freedom Fighters. And Mafia. Evil Genius too.
EDIT:
Oh! How could I forget Abe's Oddysee?

Cool. I had a dilemma about choosing just three as well, although it turned out to be easier than I'd thought.
Shoot! I left off X-COM!
About the "easy" bit -- scratch that, reverse it. :)

1. Grim Fandango
2. Blade Runner
3. Fallout 2

I'm more of a console gamer, so here are mine:
1. Chrono Trigger (SNES)
2. Half-Life 2 (PC)
3. Super Metroid (SNES)

1. ADOM: Ancient Domains of Mysteries - THE rogue-like RPG. In all it's awesomeness it features an open world, huge single-player, very good weapon and skill systems, a lot of enemies and friends, magic and divine powers, corruption to evil and much more, and requires only little from your machine. Pure bliss to play and takes A LOT time to learn to play properly.
2. Final Fantasy series. I just can't separate these because most of them are excellent. They offer hours of gameplay, vivid characters, huge worlds and pretty women. There's nothing like killing thousands of creatures to max your level and killing ultimate beasts to get the final weapons.
3. I almost feel like saying there's no third 'cause everything else is wayyy below the first and second. But well I say Civilization series, especially 2 and 4. You gotta love destroying worlds and conquering ancient civs with hordes of warriors, and making railroads centuries before it's "real" appearance.

My games, in decending order to heighten the suspense:
3. Grim Fandango: A perfectly pitched match of humor, intrigue, style, and storytelling. The art direction was fantastic and the story was even better. The story arc is over YEARS and you really get to know the characters. The very best adventure produced.
2. Halflife; I played this well after it came out but was astonished that shooters could be more than just run and gun. I am probably in the minority, but I liked all the puzzles that you had to figure out. The single most absorbing element is that the point of view NEVER leaves Gordon. You ARE him. This one small thing completely immerses you in the game. I am surprised this is not used more.
1. Civilization II: Without a doubt I have lost more of my life to this game than any other. Everything is just so perfectly balanced and fun. There is always a carrot dangling in front of you so you have to play... just... one... more... turn! Besides, what other game has taught us that you can use nuclear weapons and not only win, but crush your opponent. Of course you better have lots of settlers to clean up afterwards!

1. Lands of Lore
2. Warcraft 2
3. Gods
All of them are good old games ;)

eh... so hard to choose... so, i'll just post my top six)
1. fallout 2 (i am simply fan of this game. hooray for the immense freedom of action!)
2. elite (total, i mean TOTAL freedom!)
3. battle city (fun with friends. even now we still play it on my old dusty NES)
4. mortal kombat 2 (same as p.3, but with sega megadrive. fatalities and special moves are still imprinted in my mind in big gray pencil-scraped symbols)
5. full throttle (pity it is too short, but the atmosphere of this great quest completely covers its only drawback)
6. doom 2 (no need to explain here :)