IMHO 6x9's move a little more air and provide good bass with the nice cavity of the TR trunk. They are an easy swap with the adapter plates, although you need to insure they are not too deep (long) and hit the trunk rods.
The easiest mailorder place to get speakers is Crutchfield Audio.
I'm sure there are 1,000's of other places on the internet.
If you have a local place like Best Buy or Circuit City, you can score a good deal when things are on sale.
I'd suggest looking for a very efficient speaker. Factory stereos (other than the brand name-systems like Bose) are notoriously low-RMS output. You tell efficiency by the DB output rating.
For kicks, I tried running a factory stereo with Eclipse 6x9's. You couldn't even hear the things!
Speakers are like artwork...there's thousands of them out there and everyone likes something different. I'd suggest listening to a few brands at a local place to see what you like first. However, a key difference will be the wattage going in to the speakers. The stores will definitely have more power and speakers always sound better with more power (to a reasonable degree....)