To explain the reasoning behind this:
Upgrade your speakers, perhaps some components!
This is the core of any system, and should be first to your attention. Like mentioned, don't go cheap. If you find $20 speakers on eBay, great, don't get them. I highly suggest anyone interested in upgrading their system before asking for opinions to take a drive by a few car stereo shops, or if this isn't plausible to you, I'd only suggest Good Guys over any other poor retail store. While doing this, find the type of speaker you like (vocal, mixed, heavier on bass, etc). I suggest you bring a pen and paper along with you and write these model numbers down. You will find all this equipment almost half off online, I promise you. From here on out, you know what you like, and should pursue it, no one knows your taste, and it's extremely hard to recommend a brand as everyone likes different tones. As far as installation goes, I left this to a professional installer. Personally, I just didn't have the time to take the front doors off, and ended up paying $50 to get it done, but you could just as easily do this yourself with a little searching on the forum.
The reasoning behind doing these first, is that your stock HU can still push enough power to give your aftermarket speakers some juice, while on the contrary, you will most likely blow your stock speakers with an aftermarket HU first, while sounding horrible.
Headunit time
Once again, I suggest you take that trip around town. Looks will come into play here, but quality needs to be asserted as well. You should look for: preout voltages, RCA outputs (and inputs), compatibility with MP3/WMA, XM ready (if this is what you're looking for) and ease of use. Some claim to have 4v or even 8v preouts, some are true, some are not. The most popular and reputable brands would have to be Pioneer, Eclipse, Panasonic, JVC, Clarion, Kenwood and perhaps even Sony. Find one you like, and order!
Boom Boom
This is a toughie. There's so many to choose from, you really gotta do your research. This is where quality plays a huge part. Some key things to look for are: RMS ratings on both amplifiers and subwoofers (NOT max power), sensitivity and efficiency. Me personally, I'm a fan of DVC (dual voice coil) subs, they've treated me better than SVCs. Never overpower your subs, and in return, don't underpower. Give them what they need to function correctly. Overpowering isn't bad as long as its within a limit, but I wouldn't put a JL 1200/1 on a 400W RMS sub or some kind, if you know what I mean.
Install is up to you. I did mine myself, little elbow grease and time and it can be done in 30 minutes. Depending on your system, you'll be looking to run 8ga all the way up to 0ga wiring. I'm not even sure where else to go with this topic, it's completely huge.
Just make sure you get/build a box to the specs and tuned to your subs specs, it makes ALL the difference in the world. And I wish you good luck.
The key of any system is that if you're going to do it, do it right the first time.
Don't hesitate to use the "Search" feature here, almost everything has been covered and is answered.
EDIT:
I don't think 1 & 2 should be swapped. I had all mine done at once, but have done things this way in my friends Lightning and I'm glad I did. The stock speakers can only be pushed so far, that is, if you tend to listen to your music loud. Any aftermarket speaker will sound better on the stock HU than the contrary. I think it should be all done at once, but that's me.
