I'm with LGSONE on this one. I've had some ridiculous loud systems that blow the windows open and destroy ear drums...but unless you're competing with it, it gets old fast and is pretty much useless. I like to have a really high quality sounding system that is crisp, clear and full. My basic setup that I've done in the last few trucks I've had is to keep the speaker arrangement basically stock (believe it or not, GM put a little bit of thought into speaker placement and size) but I'll go and buy high quality speakers to replace the stock ones. You basically get what you pay for, so don't be afraid to spend a little extra on your speakers. Alpine makes a fine product that isn't terribly expensive, but if you're willing to spend a bit more, then Boston acoustics or Polk Audio have some really nice speakers IMO. If you're just replacing the stock speakers, chances are you won't need to add an extra amp for them, but if you get into the really high end stuff, you won't use their full potential unless you add an amp ( most cases you won't really need more than 100w/speaker). That alone is a really decent place to start, and will get you a nice crisp sound even with a stock deck.
Next thing I do is add a subwoofer, since stock systems are generally lagging on the low end of sound. For years and years I had a single Pioneer Premier 1200w 12" shallow mount sub. It was excellent because I could put it in a small box that fit very nicely under the seat and didn't take up a massive amount of room (I used a sealed box because I like a tight bass sound rather than a loud boomy sound). I had an 800W JL amp that had a low pass filter built right in and worked great. I could crank the bass up and it would pound the hell out of the truck, but if I wanted it to it still sounded great at low level. Nowadays I run a Pioneer 10" (Pioneer has some of the tightest sound, as far as budget woofers go IMO) in a sealed box that tucks right under the back seat no problem. Don't be afraid to spend a bit of cash on a box either. A great sub in a crappy box = a crappy sub. I run mine with a Sony amp that is built to be mounted in tight locations (I recommend this for a truck because a lack of airflow is deadly for an amp). Even though Sony is not my favourite brand and they tend to XPLOD just like the name states, I have found that if you mount it properly so it isn't vibrating all over the place, and don't have it cranked up to 11 all the time, then it will last a long long time...oh and a word of advice, more watts doesn't necessarily mean more sound. An efficient woofer of half the size can do way more, way better than something huge and crappy.
As far as a Deck goes, it all depends on what you want. Right now in my '12 silverado I just have the stock deck in place because it plays the satellite radio, has a USB port and works really nice and clean. However, if you've got an older truck and want more options than you've currently got, you can look to add something in. You can get IPOD ready decks, touchscreen, satellite radio ready, double din units, TV's, NAV units....all depends on what you figure you want. I will warn against no-name decks though. Some folks might have good luck with them, and they're awfully tempting because they seem like such a good deal...but I see them crap out all the time, and even when they're working they just don't seem to be that great. Alpine makes a good product, and as you may have guessed, I'm pretty partial to the Pioneer stuff as well.
So in a nutshell, I'd say spend half or more of your budget on replacing the stock speakers, and then divvy the rest up between an amp/sub/box, and a deck if you figure you want one.