IF YOU HAVE A MACH SYSTEM (which you probably do)
front: 5x7
Rear: either 6.5" round or 6x8
MY RECCOMENDATIONS:
Replace the headunit and mount a 4 channel amp. I went with an Alpine headunit and Kenwood amp. Ran the speaker wires to 5.25" round components up front, and 6.5" rounds in the back. Also installed 2 10" subwoofers with 2400 watts peak power from a second amp.
WHY I DID THIS:
With a subwoofer, there is no longer any need for bass to come out of your door speakers. This will make you lose the brilliance of the speakers, IMO. 5x7 will produce more mid-range and slight bass. 5.25" round will fit perfectly fine in a 5x7 hole, with an adaptor plate. This will produce near crystal clear highs, and with subwoofers there is no need to try to get more bass.
Rear speakers are going to be either 6x8 or 6.5" round. Since I have 6.5" round in mine, I stayed with a 6.5" round. But I didn't put component in the back, meaning I lost the tweeters. But since I have so much bass in the back, there is no purpose to have a tweeter back there - it would do nothing for me. Just saved me a bunch of $$ by cutting that out.
If you want to just replace the headunit and speakers, it's not as easy as you think. Since the headunit is a non-amplified output, you will need to use a line output converter, coupled with a few other things. It's all written out in a how-to on this site.