Since I have no idea exactly what is going wrong or at what point the going-wrong-edness began, I am going to relay my sad tale from the beginning, probably with more detail than necessary:
Recently my blog (www.neverslapthegiftdonkey.com) was "stumbleupon"-d and my 1000% increase in traffic caused my old server to crash and my host forced me to upgrade from shared hosting (linux server) to a VPS (centOS/Apache 2.2.3).
In preparation for moving the wordpress over, but before I changed my DNS settings to point to the new server, I exported my posts etc using the wp-admin export thing, creating an xml file. And I downloaded my entire public_html directory (including all of my wordpress files). I then installed 2.6.2 on the new VPS server (following the directions on wordpress.org). Previously I had been using 2.6.1. Using my VPS's IP address (since I didn't have a domain assigned to it yet), I ran the install.php script, set up my wordpress - imported my posts and tags and images etc and everything seemed to be working correctly.
Then my host set up the DNS to go to the new server, but when you would go to my url (neverslapthegiftdonkey.com) the browser would redirect to my IP address (188.8.131.52) and then display my blog. I went into the wp-admin settings and re-set the WordPress address (URL) from the IP to the URL and the blog address to the URL. Then when I went to test it, all of the links (permalinks, tags, comments etc) within my blog give me the following error:
The requested URL /url-name-here/ was not found on this server.
Apache/2.2.3 (CentOS) Server at neverslapthegiftdonkey.com Port 80
Since then, I did some searching, tried creating an htaccess file (no effect).