I'll second both Shogun Total War and Galactic Civilizations 2 (plus expansions). 

In addition, Medieval Total War (the real first one, not the "sequel") should be a nominee as well.  After all, at the time of its release in 2002, MTW did receive the distinction of being named #1 in PC Gamer's "Top 100 PC Games of All Time" list. 

remove demigod

put in The Setlers (at least part 1&2) and age of empires

sorry my bad. didnt reat proper

What about racing games:

Need for speed (underground 1 was my favorite)

GRID

Colin McRae: Dirt

For best storyline i would put:

Modern warfare 1 and 2

Bioschock

Baldurs gates 2 (epic game)

Prince of persia series (sands of time, two thrones, warrior within) but its sort fo pushed out now by assasin creed

For breakthru in graphics

Crysis

Anno1404: Dawn of discovery

UT 3

Heroes of Might and Magic IV

I know Age of Empires was released well before 2000.  Age of Empires II was released on Sept. 30, 1999.  Age of Empires III would be eligible...oh, right.

Also, I nominate Progress Quest.  That's an awesome game.

My nominations are:

Morrowind

Dawn of War (the first one)

Baldur's Gate 2

Battle for Middle Earth 2

Grand Theft Auto 3

Rise of Nations

(all except for Dawn of War are already listed in the OP.)

Because I'm a hypocrite, thats why    But seriously, didn't think of it.   thats a good suggestion.  (I always threw it under "rhythm game" next to Dance Dance Revolution and Beatmania, both of which had their own unique controllers and all that jazz before guitar hero did.   But since they are both 90s games, I would say that guitar hero is the "best" of this decade for that category.

nah, while I do think its funny.  I'd be too easily spotted to try something like that as a prank.   And I've spoken him personally so I certainly wouldn't PM as a mistake.

Besides, I'm the "troll" around here, and I'll call nobody else that less I risk losing the title myself.  (even though I don't deserve it as much these days as I used to.  and I claimed that title as a joke which I may be the only one that finds amusing.)

Of course it's slanted. This list is entirely based off the opinons of a bunch of PC fanboys   (No offence to anyone, but seriously, if you're on Stardocks forums, odds are that most of you perfer PC games)

 We don't prefer "PC games" we prefer "good games", and they just happen to be on PCs over consoles.  

Oh JEEZ!    you're right!!!!   that is fail on my part!   my brain threw that under '90s' game even though it came out in 2000.  yeah... thats a "best of the decade" if I've ever seen one.  F*** guitar hero or rockband. 

stealth is its own genre now?   lol...  last I checked it was at most a sub-genre of "action"

They still make fighting games?  :P   I thought they all got consumed by the "party game" genre.  

next you'll tell me "racing" is a genre.  (rather than a combination of "sports", "action", and/or "simulation")

Hey, thats not fair.   Its a port of a board  game from 1995.   That would open up nominations for remakes of older better games than the ones  already being nominated.  Its not even the best electronic version of said board game, as it includes none of the expansions, and doesn't support hotseat play.   (I'm not bashing big-huge-games, they did an alright job.  Just "cities3D" is much better)

**  disclaimer:    This post contains a lot of jokes in it.  Though some of it is mixed in with serious statements.   Interpret at your own risk.  If you feel I made any sweeping generalisms with no basis in fact, it was  likely a joke. 

Peggle hasn't been nominated? :3

I'll nominate that and I wanna be the guy. I don't think they were the best games of the decade, others might disagree though

I disagree because Catan (xbox live) actually attracted my wife to play (so did peggle but lets not go there). Any game that can attract our better half - well it deserves a mention.

I wish they had added the expansions to Catan (xbox live), but I am thinking it did not do well enough for them to bother (too bad really).

BTW, I could even add HIVE an iphone/itouch app game based on a board game (benig ported to a computer version - it is on the internet as well - probably garnered it more atention than it would have gotten on its own. And I think it is good enough strategy type game that it deserves that extra attention).

It is funny because I think turnbased games could make a comeback to a degree on devices such as the iphone/itouch. Maybe a battle version of Elemental iphone/itouch app to fool around with when one is on the plane, train or bus!

I'd like to nominate Dominions III and Disgaea.

Neverwinter Nights

The list is now up to date.

Just a couple of oddities.  You have nominated Heroes 4 but not Heroes 5.  Heroes 4 was considered a bad game by most people while I think Heroes 5 got a decent reception overall.  I certainly enjoyed it myself.  This is debateable but I personally feel Neverwinter Nights 2 also should get a nomination.  Other than the clucky interface I thought it was better than Neverwinter Nights 1.  Seems to be a big divide on this game for some reason, lots like it but a lot don't like it at all for some reason.  Just some thoughts off the top of my head.

Just looked back at some old lists and see you need Deus Ex and Knight of the Old Republic (and maybe 2 also) on your list.  Definitely at least deserve to get nominated.

I'd like to Nominate Civ 4 BTS (as a whole, since iirc u can buy it that way)

it was certainly the largest leap forward in the Civilization series, in terms of detail and gameplay. Not Sure when SMAC came out, but it was a great game

also, glad to see Persona 3 is in the runnings!! certainly would be in a close running for my vote (might want to add Persona 4 ... but then again that might thin out the Persona vote!)    

**in fact, it might be good to, come voting time, reserve the best of each genre for the places in the top 25 ... so that we don't have split-vote no-shows or consecutive results. Otherwise I suggest 2 votes per person to falsely enlarge the voter demographic!! (you can't vote three times for one game, but can choose to vote for only one, or two, or maybe three games)

in this way Fans of X can vote for X-1, X-2, and X-3, while multi-genre fans can vote for their favorite in a couple genres.

Edit: I now see that Civ 4 is already up there, but BTS is still way better :p

Since they haven't been mentioned:

Quake 3

Trine

edit:  Oops, Q3 was released in Dec of 1999, misread the instructions.  I thought it was over the last decade, not in this decade.

I nominate "Aurora", a wonderful 4X game that is not only a 4X game but a simulation that can be used to write fiction (science fiction of course).

Pros- its freeware. Its updated pretty frequently, and has a great deal of flexibility.

Cons- requires a base resolution of 1280x1024 (1280x960 is acceptable), and requires one to sign up on the forums to get the latest version.

Overall- the base resolution can be worked around with 360 Desktop and ResizeEnable (Google FTW!, both are freeware). The game is awesome, and is wonderfully interesting.

I can't believe CnC3 or Kane's Wrath didn't make it on the list....and CnC Generals did.   OMG CnC3 had me hooked for so long.

Also a few sequels:   Halo 2, for one.  Halo 2 was clearly better--that game resulted in me AND all my friends losing entire nights of sleep together at Halo parties.  And Rise of Nations: Throne and Patriots.  The replay value on RoN:T&P made it light-years better than the original.

I liked Civ3 better than Civ4.

Age of Empires 3 and Age of Mythology weren't mentioned.  I like the latter.

What about Close Combat?   I love that series, mostly because it's historical and so realistic.

Can't believe I didn't see it on my first glance over it, but Resident Evil 4 needs to be on the list. I'll probably have to make my full top 25 (or however many we are voting for) now to make sure they are all there.

pokemon silver/gold - while released in japan in 1999, they only came out in america in 2000 and europe in '01 so they totally count.

Ah, back when pokemon was cool

how has noone said Freespace 2 yet

edit: oh right 1999, I'm an idiot  (unless the thousands of mods since it went open source count??)

Check the release date on that. Not in this decade.

You're right! I was totally thinking they were pre-2000, otherwise I would have added them myself. I'm pretty sure that to this day Gold remains #4 on my list of games that I've logged the most hours on

The list is up to date, for a little while anyway.

kyogre, you should remove Age of Empires from the list, the first one was released in 1997 and the second one in 1999...

I would also like to take this opportunity to add 2 more nominees;

Medal of Honor: Allied Assault (January 2002)

Resident Evil: Gamecube Remake (April 2002).

I have a few "different" games that most here haven't played or haven't mentioned...

Tribes: Vengence (Very unique fps)

Dead Frontier (Top down MMORPG/Shooter/Survival/Horror/Thingy Majiggy)

Impossible Creatures (Oh the nostalgia)

NWN2(repeat)

Any of the Pokemon games

Final Fantasy 3 for the DS and Final Fantasy I and II for the Gameboy Advance/SP

The original Sims and all of it's expansions as released in the "Sims Ultimate Collection"

Warrior Kings: Battles (probaby made by some german company, fairly buggy, but nonetheless, fun. )