If you have the Bose, it's definitely time to dump it. If you have the stock system, you're way overdue for an upgrade. Here's what I got, and because I'm way past the age where I want to impress people with a thumping car, it's good enough for me:
Head unit: 1.5 din audiovox GC600, it has selectable backlighting green or amber, and it plays cassettes and CDs. There is a guy selling them on Ebay, for much less than the $500 that Eckler's wants, and it fits perfectly into the stock stereo opening. I don't care for the single-din stereos, I've never seen a single-din stereo installation that looked right to me.
Front speakers: 6.5" Infinity 2-way, I modified the Bose speaker enclosures in the doors to accommodate the speakers. Basically I gutted the front piece and layered it with fiberglass and then cut a hole for the speaker.
Rear speakers: 6X9" Infinity 2-way, they fit just right into the stock locations.
Amplifier: Alpine MRP-F240, it is small enough to fit right inside the passenger-side storage bin behind the seat. This was important to me because the cargo space is precious to me, and I don't want to waste it. This is a great amplifier, basically you can adjust the gain all the way up if you want to and the speakers won't cut out.
I ran new wire all the way around. This simple little system cost me only a few hundred dollars, and it sounds a lot better than the stock system. It won't thump the whole car, but it sounds pretty good to me. My next project will be to layer the interior with Dynamat or brown bread, to stop some of the road noise. This will also improve the sound of the stereo, because it will have less noise to compete with.
Good luck!