I had the exact same problem (two wordpress blogs installed on one server, and suddenly only the front page worked but none of the other ones. But it was only the pages on ONE of the blogs that didn’t work–the other one worked completely fine). I spent 4 hours pouring over my css scripts and coding in the .php files thinking there was something faulty there; I checked and rechecked every single setting to see if I had checked or left unchecked some box or option. Couldn’t figure it out.
Then I went to my plugins and remembered that I had downloaded a plugin (a YouTube/video plugin). I deactivated it and wham-bam!!! my pages started working again. So it must have been the plugin.