What's your budget? is the first Q to be asked... I'd personally reccommend some Uprated speakers for the front (they're 3.5"/87mm standard) but there aren't that many around that will slot straight in as the mounting depth is unfunnily shallow. I have some Kenwood Custom Fit ones in at the moment which work great run off the HU.
Most people seem to go with 6x9s in the rear parcel shelf, however if you're going to get a sub, I'd reccommend AGAINST 6x9s, as they will interfere with each other and you'll end up getting a muffled sound. Instead, get some higher quality 10cm speakers in the shelf supports and run off the HU. If you amp them up, you're dragging the soundstage to the rear of the car, which you don't want.
As for the HU, It's up to the budget really, as there are so many options available... I personally have a JVC MP3 CD player, for convenience more than anything...
The best bet is to stick to "name" stuff i.e. JVC, Kenwood, Pioneer etc, as the "cheaper" alternatives generally won't last as long and give a lesser quality sound in my experience.
Something like
this is a good Head Unit, as it plays MP3 and has a front Aux In so an iPod/ similar can be plugged in.
As far as a subwoofer goes, There are literally hundreds of options, depending on: whether you want a boot, music you listen to, whether you're an audiophile or a bass nut, budget.
Don't forget also that if you want serious bass from a system to put aside at least a couple of hundred for soundproofing/dynamat to give a clean crisp sound.
As far as styling, it's worth considering something like the sporting sideskirts and fully colour coding (a subtle but effective mod) you'd be amazed at the effect lowering can have, and a de-badging and the addition of clear indicators and side-repeaters.
Watch out if de-badging the boot/bonnet as there are holes under the badges, they're not just glued on.
Have a look at the
Max Power Punto Haynes Manual also for a few ideas. Also gives great advice for fitting stereo's etc
Hope that essay helps.