1) Half Life 2.
There isn't a whole lot that I don't like about it (aside from how long it's taking Valve to make Episode 3!), and there are, of course, plenty of things that stand out about it. First of all, it was made in 2004 and has graphics that easily rival those of more contemporary games. Seriously, it's five years old and you could easily argue that it's graphics are even better than some games made this year.
Also, it was one of the first games to ever implement physics directly into gameplay. The Gravity Gun is the pinnacle of physics in games. The Source Engine is a great physics engine, and this game as a whole set the bar for physics puzzles and even simple interactions in video games.
2) Star Wars: Republic Commando
I'm being serious. Maybe I shouldn't put this on here because it isn't actually one of the very best games I've ever played, but I have a good reason for loving it so. This game is the only squad game I've ever played that basically couldn't have done the squad mechanics any better. Honestly, I can't think of a single flaw with the squad system.
The biggest screamer out of all these great elements is the revival system. In most squad games, if one of your squad mates is downed, you revive him yourself, or you can order another squad mate to do it. However, if you are downed, it's game over. At least to me, this makes absolutely no sense. If your allies can revive each other, why can't they revive you?
This is where Republic Commando comes in. In this game, if you're downed, you can order your remaining squad mates to revive you, or to keep on fighting without you until the threat is eliminated. Of course, if your squad mates aren't present or if they're all downed as well, then the mission ends in failure. However, as long as there's just one man left on his feet, the whole squad can be revived. No other squad game I've ever played has actually done this. (Well, that's not entirely true. Downed players can be revived in Gears of War, but this only works in co-op.)