PROBLEM: You did a manual install of WordPress and even though your pages and posts are still listed, they all lead to a 404 page.
SOLUTION: Go to Settings --> Permalinks and change them to Default. Refresh your home page and click on a link that would have updated because of the new setting. Then change the permalinks back to the previous setting.
WHY: I honestly have no clue, but I did panic pretty badly when it happened to me. My guess is that something just got corrupt.