Id say go with the socket 939 as that is the newer of the two and so will support the latest chips.
What sort of a budget do you have?
So youll be wanting new chip+mobo and therefore graphics card as well? As new board will have a PCI express slot.
What about RAM are you thinking of upgrading this to some newer stuff or was you hoping to reuse.
You might need a new power supply as well as the old one may well not be up to the job.
Sorry thats loads more questions than answers but a ball park figure would be a good place to start from and what you want to use the system for.