3. Team Fortress 2
Development begun: ~1998
Team Fortress 2 is another example of a game that was too big for its developers' britches; the original started out as a mod for Quake in the mid '90s, and once Valve hired on its creators to create a sequel, the sky must have seemed the limit.
In a 2000 interview with Gamespot, they described everything from a bird's-eye commander overseeing the battlefield to network voice chat. The game also sported a modern military aesthetic that no doubt looked bitchin' at the time.
But Valve's focus shifted to other projects, like Half-Life 2 and Steam, and little was heard for more than half a decade. When it was finally released in 2007 alongside Half-Life 2: Episode 2 and Portal in The Orange Box, it was a very different game. Luckily, it's also a freaking awesome game, as its ongoing popularity and consistent updates attest. Unlike most developmentally challenged titles, this one was actually worth the wait. Thanks, Valve.