Pioneer DEH-80PRS head unit (Bluetooth, iPod compatibility, better sound quality than 90% of decks on the market)
http://www.crutchfield.com/p_13080PRS/Pioneer-DEH-80PRS.html?tp=5684
Kicker KS series interior speakers (full rubber surrounds, good specs, component tweeter for the front set to be installed in place of the factory tweeter)
http://www.crutchfield.com/p_20641KS464/Kicker-41KSC464.html?tp=105
http://www.crutchfield.com/p_20641S654/Kicker-41KSS654.html?tp=106
Rockford Fosgate Punch 3 shallow mount 12" subs (good power handling in a small package, deceptively big sound in little air space)
http://www.crutchfield.com/p_575P3S412/Rockford-Fosgate-P3SD4-12.html?tp=111
Rockford Fosgate Punch series amps (One for subs, one for interior speakers if you decide to go that route)
http://www.crutchfield.com/p_575P400X4/Rockford-Fosgate-Punch-P400X4.html?tp=35782
http://www.crutchfield.com/p_575P7001BD/Rockford-Fosgate-Punch-P700-1bd.html?tp=35834
As noted, all of this stuff can be found way cheaper on Amazon or eBay. I've also had good experiences with SonicElectronix and onlinecarstereo.com. You'll also need a nice power wire setup and RCAs, plus distribution blocks and other odds and ends, but I didn't list any of these as wires is wires. (As long as they're nice copper wires, anyway.) I agree with amping the interior speakers, however I wouldn't skimp on the head unit budget. Your stereo starts there, and if your head unit can't produce a good signal then you can have the nicest amps/speakers in the world and it will still sound like garbage. I have some older Pioneer Premier decks in my trucks and they were over $1k new, best part of my system though. I have personal experience with everything I listed here except the amps as I run older "made in the USA" Lanzar stuff. Rockford has always had a reputation for making nice, clean amplifiers though. (Except the Prime series, yuck) I run those Kicker KS speakers in my Suburban as my budget setup and I like them a lot.
EDIT - Just FYI I picked out that specific model of RF sub and amp to match up. The subs have dual 4 ohm voice coils so if you bought two you could wire them up to present a 1 ohm load to the amp, which can supply 700W at that resistance. The subs will take 400W RMS each so this is a very close match, similar setup to what's in my truck except I run a 1000W amp and just leave it turned down a little.