for source units, just find a cd player with an 1/8" input on the front for your ipod, that would be best. Clarion units are generally nice here. If you plan to run amps, then check the specs on the preamp outputs, the higher the voltage, the better they'll sound... in general.
Speakers, pretty much anything will sound better than stock, but I'd suggest speakers with external crossovers for your front doors. Something like the Eclipse point source series. They should fit into stock locations and the concentrically mounted components sound great for the $$. If you want more low end, add a 8" or 10" sub, but that will require an amp. Get better sounding speakers up front than in the rear... after all, YOU drive up front and that's where the sound should be coming from anyways... unless you're used to standing backwards at shows
Amps... if you decide to go that route, find something that will run your sub and at least your front 2 door speakers. MTX is probably decent at a lower price point... although I haven't heard anything from them in years. I've always stuck with Orion, but they get pricey. HiFonics is a good choice too for value, the ZX8000 (I think) was a 5 channel amp for ~2-300 new that will run your entire system.