well im one of the guys who likes rattling his own teeth out with base.
the bigest problem i had with the audio in my car is the front and rear door speakers. they are VERY shallow, and the hole in the rear is small. so, i have to make spacers for all 4 doors and i had to cut the rear door holes bigger with a saw.
if you dont want to cut, you could put 6x9's in the rear deck instead of using the rear door holes. i supose you could use both, but you could get an equally rich sound if you just bought corect speakers for your setup.
i wont be using the rear deck, i have 2 sets of a/d/s component 4" speakers for the doors that have, in my opinion, exceptional mid's and hi's. then i have 2 12" image dynamic subs in the trunk for my low's.
i went with an alpine head unit, with 3 pre outs (for my amps) i have a little more watage then i should for my setup. i have a 500w amp running each set of a/d/s speakers, and there rated for something like 100w... so i havea a little breathing room for my next set. then there is 1000w for the subs, which is perfect.
now, if you want to get subs you need to think about what sort of sound you want. if you want head pounding base, and dont really care about clarity, punch subs or rockford fosgate are about as loud as they get (for consumer market, non pro stuff). if you prefer a nice crisp base hit that actually hits a note instead of just rumbling, you might want to look at some higher end JL audio, or something simmaler to the Image Dynamics like i have.
in my opinion, swaping my head unit dident really make my speakers sound any better (stock). the new HU had a large increase in power, so i could get a louder sound out of it, but it wasent any clearer a sound then with the stock hu.
remember when budgeiting your system you will also need roughly $100 bucks in cables and fuses (power ground remote for each amp, cables for subs, speaer wire for door speakers), a capacitor if yout going to have high watage/amperage (roughly $100 per ferand. 1 ferand rated for roughly 1000w at 90 amps as i recall) your rca's which, belive it or not does not have a large say in overall sound, but how much distortion and external noise can be picked up on the trip from you HU to your amps (###### in the trunk), i spent about $100 on 3 sets of 14' RCA's. and last but not least a box for your subs, if you build it yourself you can use the left over MDF for the spacers you WILL need in your shallow door speaker slots.
hope this gets you started.
edit: oh yeah, the amps i have are Concept, im not even sure if they are around anymore, but they create very constant power, dont create too much heat, and have a descient range of ohms they can power subs at.