1. DOn't let the n00bs at Best Buy (or Circuit City, or Sound Advice, or etc) install it. If you want to pay someone to do it, research around, ask people who've got systems, etc, and find a LOCAL, dedicated car audio shop. You'll almost always get higher quality installs (I could fill this thread with all the stupid shit the above three companies have done to me, or others I've known, in regards to car stereo).
2. Generally, unless you are trying to go thug down the streeet

, then the subs aren't the most important. For a rock-based listenig pref., I'd HIGHLY recommend going with a sealed sub box, at most 2 12", maybe even 2 10" subs just to save cost (a trunk acts as a natural enclosure, so it actually gives you more thump). You want the back of the sub facing you, i.e. the front facing the rear, since you get the most bass response on the return cycle of the sub (or so I've been told by others who know alot more than me!). I have 1 10" DVC Rockford-Fosgate sub, and I'm not even running it at 1/2 the watts it can take, and I still thunder. RF subs, especially their mid-to-high end stuff, are solid, reasonably priced stuff. Can't say I know the best here, but I know the Sony Explodes ain't nothing fancy
3. For speakers, Eclipse, Infinity, Boston Acoustics all come to mind, I've owned or had friends who owned all three. I'm a big fan of Infinity's Kappa Line (I'm surrounded by them in my truck). You setup should ideally be a set of seperates in the front (woofer and tweeter), usually with the woofer mounted in the door and the tweeter on the dash, or the top corner of the door nearest the dash. Rear can vary depending on year/make/model, but usally is another midrange woofer or a 6x9.
4. As for Head units, I love my Kenwood eXcelon's, and have for years. Again, Ecplise makes solid stuff here as well. The only brand I really don't like for head units (or anything, for that matter) is Alpine, since they cost more than anyone and don't sound any better (sometimes even worse) than their cheaper competitiors....
As Sandstom mentioned, crutchfield is an excellent resource. It will help you figure out what sizes of speakers you can run in the various mounting locations, as well as custom mount kits if you don't like the options. Their prices are also fairly competitive, often times lower than retail locally. Just keep in mind that they don't stock every brand, or every model of every brand. Some of the manufacturers have good websites for researching their products. Rockford-Fosgate has a slick little install guide for figuring out how to wire up series/combinations of subs and amps, as well as a great forum for asking questions.
I listen to everything music wise (except Country, ugh), so I can relate to your last line
Something that suites my music taste yet will sound good. I still want it to play any type of music good though
. Get 1-2 decent subs, with a solid amp, so you've got good low-end (you'll be surprised how many songs have nice bass, that you never hear otherwise). Spend the money on good amps (especially the speaker amp), good speakers, and a good head unit. Especially the head unit, since it's what you'll deal with the most, and what affects your upgrade potential down the road (like if you want to add an LCD screen, PS2/Xbox, etc).