Coldfusion seems to be better lately. I haven't set the cron job up to restart the server every night but I have changed some of the coldfusion settings. It appears that a software update may have changed some of the memory variables for the 'JRun server'. Jrun was trying to take all 256mb of memory on the server and not let anything else use it. I reset it first to 128mb which helped, and now 64mb and the server's been fine since. The website seem to be performing fine but I think I'll keep watching it closely just in case.
As always, newsgroups were handy for research and I've got a few optimisation tips from them too.