I have exactly the same problem. I started a thread in the themes section because I thought it was theme related ( http://wordpress.org/support/topic/168827?replies=6#post-733866 ) but I discovered that even switching back to the default theme doesn't fix it.
Basically I followed the instructions on how to move you index.php file to the root so you can access the blog via the root domain name such as example.co.uk instead of example.co.uk/wordpress. Since then al my likks are broken and I get a 404 page not found error when trying to view any post, comment, add comment etc.
It's as though the instructions here http://codex.wordpress.org/Giving_WordPress_Its_Own_Directory no longer work for wordpress 2.5
The instructions do work in that they allow access to the blog home page directly from my domain http://www.snappyname.co.uk but all the links apart from the link to the admin control panel are broken. The whole link structure is no longer looking in the wordpress folder where all of the files remain (they haven't moved)
Foer example, I just posted a test article, which appears on the index page. Clicking the name of the article's header which normally takes you to the article tries to go to http://www.snappyname.co.uk/test/ and gives a 404 error, likewise clicking the comment link to try adding a comment attempts to go to http://www.snappyname.co.uk/test/#respond and gives a 404 error.
The links should surely be pointing to http://www.snappyname.co.uk/wordpress/test/ and http://www.snappyname.co.uk/wordpress/test/#respond
shouldn't they?
What I don't understand is that the support article says this is how to move your blog index file to the root folder whilst keeping your other files in a sub folder but it doesn't update all the link structure properly. Am I doing something stupidy wrong or is this a bug in wordpress 2.5?