(Nick Reinking nick@twoevils.org): I notice that /usr (/dev/sda2) is at 96%... Perhaps somebody can remove a bunch of the packages that are installed that we don't use?
The server is very clean in terms of software. The big culprits for disk usage are MySQL's Innodb transaction data (currently a single 10Gb file!), and logfiles from MySQL and Apache.
I don't know enough about MySQL to know how to limit that data and what the impact might be. I do think we could lighten the load on Apache log files considerably now, to save both disk space and gain some performance. For instance, we logged user agents and referrers to get some stats, but I don't think we really need that anymore.