I run Alpine Type S's. They sounded pretty good off of just the head unit. Adding an amp that does 90w RMS made them really come alive. They can be had for $50-75 online.
I have the same speakers in the front of my Impala. They currently get about 100 watts per channel with a low-pass filter installed they sound great. I couldn't ask for more from for only being two channel speakers. Plus they have lasted for 5 years in two different cars.
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.
This man knows what he's talking about
Pioneerisloud, aren't you on CACO? I feel like I've seen your name before (and laughed )
I've only signed on at CACO maybe a handful of times at best. Most of my time is spent here at OCN, and sometimes on ROE. I only sign onto CACO when I need to buy something and would like to find fair used prices.
I absolutely love my alpine Type-R's, but they sound the same as Type-S's if you don't have them on an amp.
They actually sound worse if you don't have an amp. My brother bought an S10 with type R's off the head unit. It sounds pretty bad.
What head unit though? I know running Type-R's off a stock Honda head unit sounded like crap as you mentioned, but running Type-R's (old style with big magnets) and Type-S's was about the same.
I haven't tried my new style Type-R's yet (with the smaller magnets) off the head unit, I'm using a Alpine KTP-445 in-line speaker amp with 100 W peak output per channel to power the Type-R's and they sound amazing.