Well, the problem was this...
RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule ^/favicon.ico http://xepher.net/favicon.ico [R,L]
The idea was that if a user doesn't have their own favicon.ico, it'd use the main site one, so the stupid IE browers wouldn't keep hammering for a file that's 404. What it DID do, was result in an endless loop for some reason, causing the browsers to retry several times, for every single page opened. This literally quadrupled the bandwidth, but since no actual file was ever sent, not "bandwidth" was logged by the webserver, thus making it nearly impossible to track down. Since this is sorted, I've removed the limit about outgoing http that I mentioned above. Everything should be back to normal, and hopefully, a bit faster now too.
I'll say this, after 30 hours awake, and banging my head for so long for such a simple mistake, this is going to be a facepalm I remember for a very long time! The weirdest part about it all though, is that I tested the thing, and it WORKED when I first put those lines in place. *shrugs* I'm going to bed!