Here are the seperate filesystems I use as a starting point on ALL Linux systems:
(swap) 1x physical RAM (more if < 1GB physical RAM)
/home Whatever is left
I do think it might make sense to make a seperate partition for database files, if you are running your database on the same machine as your webserver.
The main reason for seperate filesystems is to make the system more resilient in the case where something goes crazy and a filesystem fills up. This is most likely to happen in /tmp or /var. It's also useful to keep /home seperate from / for the same reason.
I put these all in an extended partition (so no restriction on number of filesystems), leaving (potentially) a primary partition for a DOS partition to hold any disk copying, diagnostic, etc. utilities. With most modern Linuxes, you don't need a primary partition at all.
I don't use LVM. Makes it difficult/impossible to use DOS-based tools. Although you lose the ability to dynamically resize and extend filesystems, you can still do so using Partition Magic or other similar tools (I use Paragon). The problem with LVM is that you can't easily manage or back-up filesystems using DOS tools. But most of the DOS-based tools DO support EX2/3 that aren't under LVM.