Alright, scanned the thread in more detail. Car audio is one thing I actually do have a good bit of first hand experience. Would like to throw my expertise out there on some of the subjects I saw.
9 times out of 10, this is your best upgrade for your buck. It doesn't seem like it. Ever. That is always the last thing in my mind that would make a difference. But, somehow, it always does. I don't know why, just something I've learned over time. Get a good one. 3 sets of pre-outs suggested. I like Alpine and the better Pioneers. Still not sure why they make such a difference honestly if you are running pre-outs, but they do.
I buy amps based on brand experience and apparent build quality. Companies that rate their amps at rms power get extra points. Don't skimp, but I don't feel you need to buy the top of the line ones either. Medium quality suggested. It'll last longer, and in my opinion sound no different than the top line.
Amplifier design is tough. I took an amplifier design course last semester. It isn't easy. I'd say the biggest determinate of amp circuitry is in reliability. When stuff fails, it better not ignite. Mid line amps should be okay for this. I personally like the old BJT amps, although after taking the class, I see why MOSFETs rule the electronics world anymore. In summary, I don't think they are all the same, but yes, they do use similar circuitry techniques.
Less important than the woofer quality, is how the woofer suits your needs. Getting a mid line woofer, and building a well made, appropriate enclosure will sound as good as a JL enclosure, and more importantly, be geared towards your tastes. Sub enclosures are tuned to a specific frequency. Remember that. You can build a sealed enclosure for more quality, ported for more quantity, and a bandpass for a mix of both and space savings. There are also some more complicated designs that use multiple woofers to use a box half the size. This is a good option if size is an issue. Isobaric reflex I think is one of the more common ones.
I don't run it in mine, but have installed it in others. Surprisingly mine doesn't rattle, but I would put it in if I planned on not driving mine off a cliff when possible. It helps mid bass a decent amount. Use it on large panels and on the doors when you take the panel off to put in door speakers. Some cars you can't skimp in this department, and it is pretty pricey. Dynamatt is the leading quality, not the leading budget. Other brands are less than 1/2 the price, and many double layer it. It basically changes the mass of the panel you stick it to, preventing that panel from resonating. It is not really 'sound proofing' your car. For smaller rattles, creative use of double back tape and spray adhesive will do the trick.
Sorry. Quality (Sound Quality - SQ) and quantity (Sound Pressure Level - SPL) audio equipment is heavy. It's not gonna make a huge difference for daily driving. I have my sub enclosure and amp rack on quick connects in my car so I can put the back seats in need be. I wired the door speakers from the back of the head unit with a relay/switch. When I am running with the sub/amps, I leave it off. The RCAs signal the amp that powers the system. When I want the back seat, I just pop off my quick connects, slide the sub with the attached amp rack out and flip the normal speaker connections back on, hence running off the head unit internal amp. This is a very good alternative if you are too concerned about saving some weight. You are **** out of luck with sound deadening though. I'd say its worth the weight just to make your doors feel more solid and luxury-ish.