I currently have all of the bose system removed and half of the new system installed. I used Sony Xplod speakers in the rear (6x9, $70) and in the doors (6 1/2, $60). Mostly because I liked how they looked and they are red so they go well with my interior. I have all of the wiring run to mount a 4 channel amp (not purchased yet) behind the passenger seat. I also haven't purchased the stereo/CD changer yet, running low on money trying to take care of the mechanical problems. So I have a big hole in the dash and will have to listen to the sweet sound of my Flowmaster 50s for a while.
I had to fab a plate to mount the front speakers and then I used some 1/8" black plastic to create a filler panel behind the speaker since the speaker is round, and cutout in the door is square.
The rear speakers mounted in the black plastic cover that was over top of the Bose speaker with some minor tweaking of the speaker grille. I had to drill a couple of holes in the enclosure to use the clips that came with the speaker. I used the same black plastic to create an edge that covers the cutout in the carpet, but I didn't create a mesh cover again because I like the look of the open speaker grille that came with the speakers.
I'm looking at a Pioneer DEH-P5500MP CD/MP3 Stereo from Crutchfield $249, and Pioneer CDX-P1280 CD changer $179. Undecided on the amp, but it will be from Crutchfield as well. I've had great success with them.
I can send pictures if you want, just send me a email because they are too big to attach here.