To anyone that has a WordPress blog installed on a Windows server, check this support thread out: http://wordpress.org/support/topic/ran-auto-update-for-31-and-now-site-doesnt-work-deleted-mait-mode-file
Otherwise, you’re going to have one heck of a time with the new 3.1 upgrade…
Or, if you’re lazy and don’t feel like reading, just install the plugin here: http://wordpress.org/extend/plugins/permalink-fix-disable-canonical-redirects-pack/ and activate it.
If you don’t know how to do that when you can’t access your blog to begin with, just type the address of your blog and put /wp-admin at the end. For example: www.myblogsaddress.com/wp-admin
Login, install the plugin and activate it, and you should be home free.