Here's my advice from the research I've done (upgrading my sound system as well).
Amp:
Depending on where you live, you can find great deals on 4-channel amps on craigslist, which will cut down cost quite a bit. Otherwise I'd go with the alpine referenced in one of the above posts.
Speakers:
I bought the Infinity Reference 6030cs 6.5-Inch 270-Watt Two-Way Component System for $100 bucks off of Amazon, with free shipping. Great deal for a well rated speakers. You probably won't need to do this, but I am also replacing the rear speakers with two more Infinity reference speakers ($60).
Head Unit: This is where you'll have to make the decision, based on the features you will want out of it. I chose a single DIN, as they seemed to be cheaper. I looked at Alpine, Pioneer, and JVC and eventually settled on the
JVC KD-R730BT on Amazon for $115. Important things you want to consider with the HU:
1. Preamp voltage - most standard HU's will have ~2v, but if you want the
best in clarity then go for a higher voltage such as ~5v
2. Features - nearly all of the $100+ HU's have bluetooth streaming as well as hands free calling, at least one USB port, an AUX port, the ability to recognize certain apps from iphones and android devices.
3. Line outputs - you will want at least 2 line outputs, one pair to go to the amp for your front speakers and one pair for the subwoofer.
Cables and extras:
1. You'll need a dash kit to put in below the HU if you buy a single DIN, these can be found for ~$10-20 on Amazon. Look up your part on Scosche's website, then search for the part # on Amazon.
2. You'll need a 4 gauge power cable for the amp. If you search for this online, make sure it is listed as AWG, so it is a true 4 gauge.
3. For the door speakers and tweeters, I went with a 50' of 12 gauge AWG cable. I ordered both the 4 gauge and 12 gauge from ebay for MUCH cheaper than Amazon, and they are true to their size rating.
4. You'll need two sets of RCA cables to run from your HU to each of your amps (the one amp powering the front speakers, and the other amp powering your sub).
5. You'll need a radio wire harness you make your life much easier, I paid $3 on Amazon for the
Metra 70-1761 Radio Wiring Harness For Toyota 87-Up Power 4 Speaker.
6. For your subwoofer's power cable, you will want to put a fuse in-line somewhere, my 4runner already had one installed but they are easy to find.
7. Lastly, tools such as wire strippers, electric tape, and end connectors for the cables make the job go a lot quicker.
Optional:
Sound deadening. I did an extensive amount of research on this...and here is what I've found. You really want at least two parts to effectively dampen sound.
1. First, you'll need a material like Dynomat. These are used to dampen vibrations produced by your tires and your engine. Now, if you're anything like me you won't want to spend $300 to "dynomat" the interior of your runner, and luckily there are some quality alternatives that people say work as well as if not better. First option is to buy some RAAMmat BXT II from
RAAMaudio - Automotive sound deadening products. Second option is to get something like edead from elemental designs. Edead is cheaper, only $1 a square foot, but isn't as good as RAAMmat. Edead would be ranked good, RAAMmat would be ranked better.
2. Second, you want some kind of foam. Raammaudio sells their complementary ensolite, but again I looked for something cheaper and just as effective. I ordered some closed cell foam, made specifically for sound dampening, from the Foam Factory. It's designed for sound studios, but will work just as well in a car (you'll just need to use your own adhesive). For $50 including shipping I got enough to put in all my doors, some floor space, and some areas of the firewall. It's important that you looked for closed cell foam, as it dampens sound better, is more durable, and is resistant to moisture and mildew. The thicker the foam, the better the sound insulation. I have also read of some people ordering Roxul Safe'n'sound from Lowes (designed for homes, but should work equally as well in vehicles if properly applied).
You will want to apply the dynomat/edead/or BXT II first. Focus on flat metal panels, as those are more prone to vibrations (curved metal is structurally less prone to vibrations). You don't need full coverage, I plan on applying between %50-%75 coverage. Then you adhere the foam on top, with more coverage (including curved metal areas).
I'm installing all of these this week, so I'll create a writeup with my experiences with the process, and my final opinion on my "custom" sound deadening technique. If anyone has anything to add or correct, feel free as I don't have time to proofread this post