I personally would start afresh with a newer operating system (Snow Leoaprd came out in August 2009). Additionally, if your hardware is that old, I would be concerned about it too if it is a production server. Problems tend to creep in on a server over years of service and it is good to get a fresh update of the OS. There have also been issues with Snow Leopard only working with Java 6 and not Java 7. My recommendation would be to upgrade to 10.8 and get a fresh server going. FileMaker Server 11 works on 10.8 just fine and there is better security in 10.8. But if you're going to the trouble, have you considered FileMaker 12?
Thanks for the comments. I am in the middle of an 11-12 migration to a different (newer) server. This one only had a few web-enabled databases that I am planning on converting soon.
Right now I am on a different continent from the server so can't do a full OS re-install (this device won't run 10.8). But I will probably have to go that route when I get back to physical control of the server.