I think there is some advantage with NTFS especialy when the computer is a shared one as the directories and files can be better protected. For me I intend on using FAT so I can read and write to both partitions from either OS. If NTFS will allow from both OS's then I'll be going that route then.
I have an old 200mhz machine that I have thought about setting up as a local webserver to test things on using Linux. This all is to get a feel for the OS before I go and set up a machine to colocate somewhere. (and to be able to test scripts locally too)
