In settings, discussion, do you have the boxes at "Before a comment appears" unchecked? And you have settings, discussion, "Allow people to post comments on new articles" checked?
If so only comments with too many urls (check that setting) or words in the moderation or blacklisted area should be the only ones effected.
Have you tried:
- deactivating all plugins (yes, all) to see if this resolves the problem. If this works, re-activate the plugins one by one until you find the problematic plugin(s). Don't forget the ones in mu-plugins. If you can't get into your admin dashboard, try resetting the plugins folder by FTP or PhpMyAdmin. Sometimes, an apparently inactive plugin can still cause problems.
- switching to the Twenty Eleven theme to rule out any theme-specific problems.