Well, in my car I have a pair of 6.5" Infinity components up front running off the headunit (Pioneer DEH-P80MP).
I also used to have a cheapo 10" sub in a sealed box, running off a cheapo Mutant amp. It was a very budget setup (apart from the HU) but the overall sound was very detailed with nice tight bass.
Since I got rid of my sub, I've had the speakers faded 3/4 to the front and honestly, don't miss the rears at all. Of course, I now need to deaden my doors properly to stop all of the rattles and vibrations that the sub covered up.
The reason I don't like 6x9's is because they do nothing for the SQ. Sure, they go loud and have loads of bass, but that's about it. They drag the soundstage backwards and have terrible quality midrange and treble... very harsh on the ears.
What you reall want to do is keep the standard rears, get a nice pair of front components, a few sheets of Dynamat and amp the front speakers. Get a good quality 10 or 12" sub... unless you want LOTS of loud bass.
Seriously though, if you get 6x9's and a cheap sub, people will laugh at you as you come down the road. Whereas with a good quality install that's been setup properly, you won't draw attention to yourself/your car but when people do get in and hear the system, they'll comment on it.