From the beginning Joel made a simple assertion: Hire great people, give them a great environment, then sit back and watch them kick ass. He said this before all of this became conventional industry wisdom (and probably played a major role ushering it in). With products like CityDesk, FogBugz, and Copilot failing or seemingly meandering, it didn't really seem like much would come of it. But they kept at it and look at them now. I guess good software does take ten years (give or take) [1].
Of course it didn't hurt that Joel is one of the best bloggers who ever done it, and I'm sure at least Stack Overflow benefited tremendously from being seeded with Joel's captive audience, but they have still executed the hell out of it and continue to do so, and obviously continue to spawn awesome stuff on the side.
[1] http://www.joelonsoftware.com/articles/fog0000000017.html