1) Wasteland
2) Fallout 3 (it's in the top 3 as of this posting, that may change as I get further into it)
3) *hasn't been released yet*
It was very hard to decide whether to give spot #2 to FO3 or not, but it's there so you know my decision. Saving #3 obviously for something that hasn't been released yet.

1) Super Mario Bros. 3
2) Sam and Max Hit the Road
3) Okami

1) Tempest
2) Syndicate
3) Quake 1

I couldn't pick just three so here are my favorite new, and favorite old games.
New Games:
1. The Orange Box - I know this is technically 5 games but since they are all made by Valve and they all share the same engine, you could regard them as one really big game with different gameplay 'modes'. An epic, story driven mode; a fast and brutal multiplayer mode; and a short but sweet puzzle oriented mode. It's also the best value in gaming, period.
2. STALKER/Clear Sky: I love these games for their challenge, atmosphere, and realism. In my eyes they can't be matched in any if those areas. There may be some bugs at first but after a few patches these games really shine. The mod community has been really enthusiastic, I can always count on there being some astounding mod for me to install after the original gets stale.
3. No More Heroes: This was a tough choice but this game just can't be beaten in pure, maniacal, slice you in two with a beam katana, fun. There are all these little quirks to the game that keep me coming back for more. Like the fact that when you decapitate a foe he is still somehow able to yell out "MY SPLEEN!". The combat, boss battles, side missions, etc. all come together to make one incredibly entertaining package. It's the only reason I haven't pawned off my otherwise dust-collecting Wii.
Old Games:
1. Starcraft/Brood Wars: No explanation needed really.
2. Duke Nukem 3D: I know it could be considered a Doom clone, but it's just so damn... KICK ASS. Face kicking, alien shrinking, stripper tipping fun.
3. Jet Force Gemini: Hands down, my favorite N64 game. Hard, action packed, gory (ant decapitation), great music, great graphics (the best on the N64 imo), and LONG. This game tooK me forever to beat when I was younger, and it still takes me longer than most to beat.

1. Unreal (PC) - before Unreal I've played lots of Doom, Wolfenstein, DN3D and Quake. But Unreal was the first FPP game, hell, even first 3-D game to make such a huge impression on me. I realize its flaws (stages become slightly rushed towards the endgame), but I'm still replaying it and still enjoying it.
2. Perihelion: the Prophecy (Amiga) - whenever someone tells me that a game has a good post-apocalyptic feeling, I tell them to play this. Because, you know, there might actually be a chance they will. Perihelion is a gothic-cyberpunk RPG hybrid. The world is dying, there are malevolent entities and there's a party of six warriors engineered to counter this. The game's short (about six hours) and difficult, but it has enough style to trump all other cyberpunk and post-apocalyptic games *combined*.
3. Wizardry 8 - the last old school cRPG, and a great one at that. Party of six, a rather large world to explore, and hordes of monsters lurking at every turn. Multiple races and classes, as well as their versailty allows lots of replay value (including solo games).

- Gothic 1
- The Need for Speed
- Age of Empires

top 3:
star control 2
planescape: torment
Freespace 2
Honorable Mentions: (tooo many!!)
MOO II
Deus Ex(s)
System Shock 2
baldur's gate(s)
wing commander(s)
half-life(s)
Lands of Lore (s)
Monkey Island (the first one)
Fallout(s)

Portal
System Shock 2
Deus Ex

1. Planescape Torment
2. Silent Hill 2
3. Deus Ex

1) XCOM TFTD
2) FALLOUT 2
3) Baldur's Gate 2

1. Red Baron- the original from 1990 or '91, no one has topped the dynamic campaign system of this beautifully done flight sim to this day. I love this game like I love few other things, easily my favorite game of all time. For the time it came out, it just did everything perfectly, possibly the only game I'd give a 10/10 score to.
2. The Marathon Series- relatively unknown shooter series by Bungie developed for the Mac, didn't come out on the PC for several years IIRC. These mixed the action and gameplay of Doom 2 with a storyline similar to System Shock 2, and easily are my favorite "shooter" games to this day. I still play and so can you for free (legally), just search for "Marathon Aleph One". They're still nice looking today in 1280x1024 resolution with 2x anti-aliasing!
3. Mortal Kombat II- The game I was so devoted to that I reached a point of fanaticism as a kid. I knew just about every special move, fatality, and etc for every character by heart, and could beat just about anyone with almost any character. I had an MK shirt, necklace, lunch box, posters- you name it, I probably had it. I even wrote a letter to the woman who was the digitized portrayal of Kitana and Mileena (Katalin Zamiar, she has a bunch of martial arts training material out now, still hot too, search for her!), and got one back from her, which I framed. I still play it often, though I'm nowhere near as good at it as I used to be, since I don't eat, sleep and breathe the game anymore.
Oh, and contrary to what the politicans who wanted to ban/censor MK 2 said back when I was a kid playing away on it, I haven't gone on a mass murder spree yet, tortured any animals, or ever thought it would be "fun" to try and rip my friends' heads off in reality. I'm sure these same vote-whoring professional liars just loved the Grand Theft Auto games as well.

1. Populous 2
2. Syndicate
3. Castles 2
errr.. wait... I can think of a heap of others that I like just as much as these. The whole "name 3" idea is broken.

1. Half Life 1
2. X-COM: UFO Defense
3. Fallout 1

X-series (can't choose from them)
Homeworld
Nexus: The Jupiter Incident

1. Final Fantasy VII
2. Goldeneye
3. Forza 2
Honorable Mentions (no particular order):
Knights of the Old Republic
Perfect Dark
Perfect Dark Zero
Final Fantasy 2 & 3 (IV & VI in Japan)
Dirt 2
Left 4 Dead
Command & Conquer Series (before EA)
Zelda: Ocarina of Time