I'm work'n on my system now (my fast is 4 days old now)......its a really broad question to ask man ;D
Do you want a single din? Double din? Do you want to replace the speakers? What type of music? You a bass hound? or just enough to fill/make the music pop....what's your budget? Do you want NAV/DVD ect...?
First you gotta get something like this:
(pic from ebay)
It can handle both single or double....then you gotta pick outta the million HU's out there....and build your accessories from there depending on what your HU can handle...then pick out your amps ect..
Its overwhelming but so much fun at the same time! 8)
I'm go'n with a 7'' double din screen (AVIC-D3 most likely), custom sub box in the spare tire well, no idea where I'm mount'n the amps, ipod intergration, blue-tooth, so I can drive crazy and not worry about the phone crap

....I'm gonna pull the audio no no and not replace the stock speakers yet (as I read they are molded in and don't wanna fight with that right now), if the snow cones are that bad, I'll replace them shortly after...
Prob not all that much help