The only thing I would porbably change is the hard drive on it. Since Sata Drives are cheap. a 2 terabyte hard drive in Canada you can pick up for is about $75 new over here. That way you have more than enough space for it. And check to see if your PCIE can be used in there as well. Somce Dell computers have hat looks like daughter cards for the PCIE or a smaller version of it that makes it look like a half height on it.
I'm looking at the specs roughly here from dell at this link http://support.dell.com/support/edocs/systems/dim3100/en/sm/specs0.htm#wp1052310
I know my lenovo I can still add in a PCI video card in it or change the current hard drive that put in there from a 500 gig to a 2 terabyte drive in it if I need to. But the amoutn of disk space that I really need is not worth upgrading on my lenovo thinkcentre over here. At least go with a change of the hard drive at least.