Pickups would be the most drastic change in tone (obviously). If you're going for appearance, besides refinishing, a hardware change would look cool. Either gold or chrome would be a nice alternative to the usual (and sometimes boring) black. Also, you may think about replacing the factory nut with something of a more quality material (such as bone or graphite). As you also stated, custom electronics such as quality pots/jack would be a good addition. You could also change the
pickup rings to match your hardware. Straplocks are a good security addition. If you're really with this guitar for the long run i'd also check out some finish options and inlay work. Our vendors, found at the top of the website, do great work.
Good luck,
Jon Kon
Didn't see JN's post until after i posted. He's got the right idea also...