Don't put a general purpose Web server in one big partition! Consider disaster recovery. If you get rooted, you might want to replace root and /usr but leave /var. To avoid getting rooted, you might want to mount noexec any directory Apache can write in. Make a partition for /tmp, /var/tmp, Squirrel Mail's data, Mambo's data, /var/log/apache, etc.

Over time your users will install badly written PHP applications and they will get exploited by worms and skript kiddies. The exploits will write spam-mailers and attack programs in /tmp but they won't run. It won't stop a determined attacker, but the kiddies will move on to lower-hanging fruit.