I upgraded WordPress from 2.5.1 to 2.6 last night — and just discovered that the permalinks to articles are now broken. You should be able to click on the title of a post, and be taken to a page that has that post and nothing else on it. Instead, you get “404 — File not found”.
Damn.
[Update]
Ah. According to the WordPress support forum, this is a bug in the 2.6 release.
I used this workaround:
…On the Settings->Permalinks screen, add some values in for the category and tag bases. The words “category” and “tag” will do just fine. As long as they are not blank, this should work around the bug.
Weird, but OK. That did indeed make the problem go away.
This should be fixed in the next release, 2.6.1.