T has this one pretty well nailed down, but i'll throw in my four or five cents. For the HU, I vote either Pioneer, Kenwood, or Alpine. If you spend about $180 you should be pretty well set with remote, preouts, all the bells and whistles. Before you buy, play with it and see if you like the interface, that type of thing. Also, try to get rms wattage per channel. Most of them will advertise like 50x4 or 45x4, but the real numbers can range between about 20x4 to 30x4. When I bought mine, it's only 180w, but it puts out 24x4 rms which isn't bad for $140 deck.
Moving on to speakers, your jeep has 3.5's in the dash, then 5.25's in the doors and back. 3 pairs rather than two is going to hurt your wallet, but just shop around and you'll be ok. Again, Pioneer and Kenwood make some good ones for a decent price. Infinity is another of my favs, but that might get expensive. I recomend 2 ways all around, you don't need any 3 ways since you have 6 speakers and that'll save you money.
Regarding subs, you've got lots of options here. The pentagonal sony's, i have heard a pair of them and was not too impressed. They might sound ok if you have 4, but you can find better with a little looking. I've heard good things about Alpines and MTX, avoid Bazooka. I was a fan of Infinity subs, but then someone on this board told me he kept blowing them up at moderately high volumes, and that recently happened to a friend of mine.
Now for the important part - amplifiers. Like T said, this will eat up your money. And also like T said, avoid Legacy and Boss Audio. You're going to be looking at 150-200w rms per channel depending on the subs, and it'll be either 4 channels or two 2 channel amps. Alpine puts out some nice ones, but you're going to pay since you need that much power. I recomend Lanzar. I own a Vibe 420, which is 100x4 rms, and retails $140. Check out
http://shop.store.yahoo.com/mobile-emotions/lanzarvibe.html and take a look, you could get a 125x4 or maybe a pair of 200x2. When you're looking at amps, make sure you're looking at rms wattages, not peak. Companies advertise peak numbers because they're higher, but the peak value is just about worthless. Whatever subs you get will have a recomended rms rating, and you'll want to match that as close as possible.
To finish up, let me do a run through of how well I spent your money. Let's be generous and say you get a $200 HU. Let's say you get $40 Infinities for the dash, then two pairs of Kenwoods at $60 each. For your subs, you could get a pair of MTX RoadThunder 10's for about $140, you want two pairs so that's $280. Then for power you could get a couple of Vibe240's at 200x2 for $240. If you go to WalMart, they have wiring kits for $25. Grand Total of $930, not too far over budget. Shop around and you could probably nail a setup like that close to $800. Good luck.
I refuse to tiptoe through life only to arrive safely at death.