If you want some of the best 6.5" speakers you can buy.
Be prepared to get a 250w RMS per channel 2 channel amplifier to power them though (more than your subs will take). And also be prepared to do some custom fiberglass work to make them fit...as those speakers are 6.5" in diameter...and 7" deep.
If you want some good speakers to run off a head unit:
Alpine Type S
Rockford lower end lines (not the power series)
Good speakers off a real amplifier (not some cheap amp like you have now):
Alpine Type R
Rockford Power series (model has a T in it)
Hifonics Brutus (not my first choice, but not bad)
My personal favorites would be the Alpine, Rockfords, the RE XXX of course, MB Quart, or Infinity's. Make sure you get component speakers for up front, coaxials in the rear. And you only need to amplify the front speakers. Don't forget sound dampening material in your doors either, if they're door speakers.
Get your speakers and a good 2 channel amp to power them (I can make some recommendations based off your speaker choice). From there, worry about your subwoofer setup. You could build up a single 8" subwoofer that'll absolutely BLOW AWAY your generic 12's you've got now.
Oh, and go check out sonicelectronix if you're in the States.
They're the newegg of car audio. Woofersetc is also good.