Like Mark, my old web site had a small /boot partition and one big /root partition. I had a couple of extra drives, each with one sole partition, from which I served up web pages, etc. The only thing that lived on the root partition was the OS. While it wasn't a database-backed site, it was serving up half a gig per day and getting hundreds of thousands of hits and it had no drive latency issues.
From a performance standpoint, your biggest gain will be from moving your web/db stuff to a second drive. No matter how clever you are in partitioning a drive, you still only have one disk spindle and one set of drive heads. A bunch of small, fast drives is better than one heavily partitioned big drive. Naturally, if you run out of space on a small drive, you can get a bigger one and move the data with a tar pipe. Changing partition sizes on a drive is a sysadmin headache.
