For any of you out there running Abyss Web Server (like I am) and have WordPress installed (184.108.40.206 for me) and cannot get the permalinks and categories links, etc. to work correctly, I have a solution.
Open up your Abyss console webpage and go to your scripting parameters. Click the pencil icon (edit) on the line that contains the path to your php interpreter. In the next screen make sure that it is set to "Standard" and not "PHP Style."
Then, open up your wp-blog-header.php file. In the first part of the file you'll see a comment that says "// Process PATH_INFO and 404." On the 2nd, 3rd, and 4th lines after that line, change where it says PATH_INFO to ORIG_PATH_INFO. After that you should be all set.
If for some reason that does not work, you may need to replace more/all occurances of PATH_INFO to ORIG_PATH_INFO.