If you want to do some real reading and research I suggest signing up and reading both www/diymobileaudio.com (more SQ oriented community) and also
www.caraudio.com (more SPL oriented community) both have HUGE classifieds where if you are patient you can get a good deal on almost anything out there. Now for new stuff, sonicelectronix linked above is a good place, crutchfield.com is great for research but bit pricier. Also as said it is very budget dependent.
Now for an HU, I am an Alpine fan but I hate to say it for 90% of users you will get more for your money going with either Pioneer or Kenwood in the Double Din nav department. Alpine has great expandability if you want some killer tuning options, but you could also use a different processor on the other 2 units if you wanted to get that involved.
For speakers I would put some 6.5" components in the front (just skip on using anything oval). With this the hardest part is finding a space to mount the tweeters. If you stick with passive tuning it is best to keep the tweeters within 6" of the mid so that the path lengths (distance the speaker is from your ear) don't become too far apart causing seperation in the music playback.
Subwoofers are what everyone puts the most emphasis on, and we are very short of space on where to mount them in these trucks, even shorter if you have a power sliding rear window. Again budget will be key here, but basically without going wild you have the option of behind the rear seat, under the rear seat, or center console. Up front bass is amazing from the center console but its not for everyone as it is a little more install intensive and fewer options, but opens up options for amplifier location. Behind the seat and under the seat will both be similar selections of shallow mount subs, with some very few conventional subs being able to fit behind the seat (10's and 8's only)
After you get that all narrowed down you can start amplifier selection to work with what speakers your running. Or go backwards to see what amps you currently have and want to use and tailor your speakers around that. Try and get the power ratings close but they don't have to be perfect.
Focal sure makes great speakers, also check out Hertz (HSK165's are a nice set) the pioneer Premier sets are nice, as well as the Alpine Type X, but this is where it helps to audition them before you buy them as each will have some slightly different sounds, particularly the difference between silk and metal dome tweeters (mellow vs bright.) For amps I personally really love my Sundown Audio amps which are pretty well priced for what you get. Then subwoofers are going to be very dependent on budget and installation location, for prefab behind the seat boxes check out
www.spl2k.com