World of Warcraft
We don't have Everquest. We don't have Ultima Online. We don't even have Guild Wars. We have no MMORPGs right now and the things you think they "suffer" from are the things that millions of players like about them. How can this be a valid list when a whole genre is being written off? No MMO has ever appealed to me to the point that I'd want to invest months into it, but having tried out several I must say that WoW is easily the best designed. After trying every class they were all unique and fun, and a cooldown system (and just smart design) allowed you to use all of the skills you have (at least up to the point I played, but we're talking 10 or so skills to manage which is very high).
Call of Duty 4
I've died a couple hundred thousand times in video games. But you don't really experience death until you are crawling from the wreckage of your downed chopper, skin melting from radiation. Nothing is comparable to the desperate last stand as your comrades are one by one executed by the villain. There is genuine art at work here.
Diablo 3
If we are arguing for redemption I'm going to suggest Diablo 3 again. It's new, and many people are still blinded by nostalgia for a 12 year old rpg. If you want just the best games on your list, you want Diablo 3. Freeing up resource systems, giving players more than two different abilities to use at once, getting rid of basic attacks, the absolute variety of 125 abilities per character before passives, the fact that all abilities scale, the lack of dead levels, the introduction of cooldowns and other systems to encourage diversity (generator/spenders), that is 7 things that every Diablo clone should have from now on. Diablo 3 is one of the biggest improvements as a sequel ever, and should be seen as a genre changer.
Dragon Age: Origins
Dragon Age: Origins. Who the fuck voted no? Ok, I'm not Bioware's best friend at the moment but Dragon Age was the best Bioware game, and even really the best d&d esque fantasy game ever made. This is another prime role model for RPGs (one that the above Diablo 3 may have taken things from), requiring a great amount of strategy. You could script your allies and use a variety of abilities diversified by cooldowns. The mechanic for active abilities was genius. Each class had a variety of builds you could use, and damn that mage. Dragon Age is THE video game for playing mages. Then there is the surprisingly fresh story and always great characters. The ending even delivered. Remember when endings could just be good and show you what the effects of your actions were? Good times.
This was also right before you switched back to open voting, and there are quite a few questionable games left out in that vote (Skyrim, Fallout 3, some others).
Oregon Trail 2
Simply put we ended up with more yes votes than no after the deadline. Rigidly enforcing deadlines like this is not going to lead to a more accurate list. I don't know how many other games would survive if we went back and did housekeeping, but when it concerns the series that introduced many kids to computer gaming yeah I'll speak up about it.
League of Legends
Let's not delude ourselves as to why both this and DotA lost. There is a big pissing match between fans of both games. Well I voted Yes for DotA and was the person who even argued for it to be kept in the pool at all, so if anyone feels like bringing their fanboy bullshit into this they can suck my dick. LoL has dozens of Smogoners playing it every day who can come in and vouch for this game. It really is a genre unlike any other, and one of the best multiplayer games I have ever played.
Other games I'll chime in on later;
Civilizations 5
Marvel vs. Capcom 2
Metroid Fusion
Prince of Persia; Sands of Time
Resident Evil REmake
Skies of Arcadia