Deck: Pioneer DEH-4200ub
Doors (all 4): Polk db651's
Rear roof: Kicker KS410's (4x10's, weird size. Kicker is the only major brand that still has 'em.
Amp: Used JBL P80.4 from Craigslist
Sub: Pioneer TS-SW841D (8" shallow mount sub)
System is pretty mild. I ran the doors on the front left and right channels, so I still have left/right balance. Ran two speakers per channel to get to two ohms and 80 watts each. The rears are just powered by the deck. The sub is running off the bridged rear output, so it gets 160 watts. I also ran the RCA cables from the sub output on the deck to the rear input on the amp, so I have individual sub control. I love the system. Very clean, crisp sound for rock and classic rock, which is what I listen to. I used a sealed box to get crisper bass hits.
The main thing I love about it is that all this is under seats, so you can't see it, and I can still use my truck the same as before I had it. Didn't want to put anything in a big box in the back, because I still load stuff up in this thing, so it wouldn't be too practical. Besides, then, no one sees it, so they won't try to break in to steal anything.
Personally, I love everything I have. The deck is great, and the usb charges your iPod while playing it, so I never listen to CD's or radio any more. The Polk's get pretty loud without any distortion. I would suggest getting a 4 channel amp and running two channels to component speakers, and then bridge two for a sub. Just make sure it's an amp that tends to run fairly cool, just gives you that extra peace of mind. I say only one amp because it really reduces clutter, and does the job for a mild system. I would say that you should run your components off the amp, because they can go much louder without distortion, and it helps balance out the sub. Just make sure you match the RMS on the speakers/sub with the output on the amp and you should be fine. Also, make sure the amp is 2 ohms stable if you want to run it that way.