you could start it fah4 with "nohup" like this: "nohup ./fah4" assuming your currect directory is the directoty fah4 is located in.
then just close the window, and it will keep running in the background.
if you want to see its output you can either open the file nohup.out which will be in the folder u were in when u started nohup, or by opening ~/Library/Folding@home/FAHlog.txt
or you could just start it like the above poster suggested(with crontab).
i made a VERY simple F@H menu extra, that can only stop and start F@H, but thats all i need to be able to do.
if you got 2 clients running it will stop both, there is no way of telling it to only stop 1 of them, here is it:
F@H_Menu_Extra.menu.tgz (requires MenuCracker or Menu Extra Enabler, only tested with MenuCracker)