phils and V's will cost you about as much as a frame upgrade unless you're thinking big.
to be honest, though, i'd save both for later.
a carbon fork and seatpost will be a much smarter upgrade on a commuter.
if that's the stock fuji track headset, i'd swap that out too-- go with an ultegra headset.*
much much (much) smoother and won't need the maintenance the stock one will.
after that, go with wheels. you'll get way more out of wheels for the money you're looking to spend than you will for a frame at that price point.
consider a radial laced front, three cross rear.
and good luck!
*if you really want to start having fun, swap the headset out for a threadless, get a new stem and go for a full carbon fork (or at least one with an aluminum steerer). with your threaded setup, you'll be restricted to a cromoly steerer. not that there's anything wrong with that, but it's something to consider.
Last edited by sp00ki; 12-31-08 at 01:38 AM.