As many of you will have realized, the Penny-Arcade forums were down for a number of hours today.
For those of you who care about the details, I've been told the exploit originated at another site on the cluster. I was concerned that there was an as-yet-unannounced phpBB exploit which is what prompted me to take the forums down despite the fact that the only thing missing was the index.php file.
Interestingly, it is due to penny-arcade still using the legacy .php3 (rather than .php) notation on it's front page that kept that from being overwritten as well.
There may be some quirks with the index page because it may be missing some recent changes. It looks "off" to me, but I'm not sure what about it looks wrong yet. I didn't do much to that file, though, so it shouldn't be anything terrible to fix.