Ever since I went to college in fall '07, I simply stopped investing into a PC gaming.  Simply put, I had less money to spend on PC parts, less time to invest into research and made a propriety to have a Laptop for portability (at the time, I was traveling to school and back 4 hours a day).  In addition, My father was paying for my Laptop, and simply put, he hates desktops.
 
So my old computer broke, died, and was replaced under my old warranty policy.  The computer I have now actually makes for a pretty good gaming PC, in addition of some nice extra features such as a Blu-Ray player and a few other things.  While there are some games it can't play at all (such as Mass Effect 2), there are quite a few games I can still play.  That being said, anyone care to help form my list.  Also, please help filter bad, overrated games.  I'm not a Graphics whore, I prefer gameplay.  In fact most of my old computers I used to build were minimum specs. I'm also tolerant of controls, but I am not looking for something to be completely fucked up.  But I do want something that works out of the box.
 
List
-The Orange Box
-BioShock
- BioShock 2
-Civilization 1, 2, 3, 4
-Call of Duty 4: Modern Warfare
-Call of Duty 4: Modern Warfare 2 (Steam Version)
-Warcraft BattleChest
-Starcraft Battlechest
-Diablo Battlechest
-System Shock 1 and 2
-Splinter Cell, Chaos Theory, Pandora Tommorrow, Double Agent, Conviction
-Crysis
-Dragon Age Orgins
-Fallout 3
-Black and White
-Empire: Total War
-Left 4 Dead 1 & 2
-Guild Wars
-Rise of Nations
-Battlefield Bad Company 2
-Age of Empires, 1,2, 3
-Doom 3
-MechWarrior 4
-Thief 1, 2,3
-Gears of Wars
-Halo 2
-Boarderlands
-Torchlight
-Prey
-Crimson Skies
-Aquaria
-Napoleon: Total War
-Quake 1, 2, 4
-Rollercoaster Tycoon 3
-Rome: Total War
 
More Suggestions are welcomed.
 
Also Here are my specs for those looking.
 
 OS: Windows 7
CPU:   AMD Turion(tm) II Ultra Dual-Core Mobile M620  
CPU Speed:  2.49 GHz Performance Rated at: 4.6065 GHz  
RAM:  3.7 GB
Video Card:  ATI display adapter (0x9712 
Video Ram:  1.9 GB 
Pixel Shader: 4.0
Vertex Shader: 4.0 

Good list! :)
I recommend that you also get X-COM: UFO defence, all Sam & Max episodes and Dawn of War 2

Pretty good list. Here are a few games I'd recommend you check out:
-Mount & Blade: Warband
-Penumbra: Overture and Penumbra: Black Plague
-S.T.A.L.K.E.R.: Call of Pripyat
-Tropico 3
-Batman: Arkham Asylum
-Killing Floor
-Plants vs. Zombies
-Trine
-Braid

Posting your specs would help a little. I just finished DA:O on the PC (played on my partitioned macbook) and yes its pretty buggy in some parts (Awakening especially) and yes everyone has wooden teeth but its totally worth a look. Im just going to reccomend Heroes of Might and Magic 5, Warcraft 3, Age of Empires 3, Empire Earth 4+, Civ 4, and (if your computer can handle it) Dawn of War. Mostly I'm reccomending these cus they're PC exclusive. There are a lot of console ports on the PC that technically look better but are also kind of a mess so you might want to stick with the console versions for them. Try and narrow your scope to games made for the PC and you can avoid a lot of headaches from sloppy ports like GTA4. In a perfect world the PC version of every game would also be the best version but its not a perfect world.

" Posting your specs would help a little. I just finished DA:O on the PC (played on my partitioned macbook) and yes its pretty buggy in some parts (Awakening especially) and yes everyone has wooden teeth but its totally worth a look. Im just going to reccomend Heroes of Might and Magic 5, Warcraft 3, Age of Empires 3, Empire Earth 4+, Civ 4, and (if your computer can handle it) Dawn of War. Mostly I'm reccomending these cus they're PC exclusive. There are a lot of console ports on the PC that technically look better but are also kind of a mess so you might want to stick with the console versions for them. Try and narrow your scope to games made for the PC and you can avoid a lot of headaches from sloppy ports like GTA4. In a perfect world the PC version of every game would also be the best version but its not a perfect world. "

You might want to check the Humble Bundle as it includes Aquaria that you listed and Penumbra Overture that  yinstarrunner recommended. Also, by getting the humble bundle you get a discount code to get all three Penumbra games for 5 bucks.  And remeber to log into Steam to get Portal for free.
 
A few recommendations:
- Braid
- Trine
- World of Goo
- Sam & Max (all three seasons)
- Torchlight
- Altitude 
- Dragon Age: Origins
- Machinarium

Also, don't get Splinter Cell - Conviction if you don't have a stable internet connection.

• Theme Hospital 
• F.E.A.R.
• Clive Baker's Undying
• Lucidity
• Deus Ex
• Vampire The Masquerade: Bloodlines
• Baldur's Gate 1 and 2
• Knights of the Old Republic
• Knights of the Old Republic 2
• Fallout 1 and 2
• Sanitarium
• Mount and Blade
• Sid Meier's Pirates

Company of Heroes, Red Orchestra: Ostfront, Beat Hazard, Command & Conquer Series, Dawn of War (Will definitely run on your laptop), Medal of Honor: Allied Assault, Counter Strike, Day of Defeat, Warlord, Dawn of Discovery and Flotilla. 
 
Company of Heroes, is the only one that might be a stretch but there is a SP demo.