There are some great reccomendations in this thread and for $1,000 you can do pretty well in a truck. I don't recommend going with ebay for anything as it has already been pointed out most sellers on ebay are not authorized retailers so technically you don't have a warranty on your products, and especially with a company like JL you may not be getting brand new stuff. Best to buy from authorized retailers. Online Sounddomain and crutchfield (can be pricey but if you look has some good prices from time to time) are good choices.
Make sure you include door speakers in your system because if you don't and you keep the factory speakers in there its just going to sound muddy and not nearly as good as you want it to.
What do you want out of your system? SQ or SPL?
JL Subs and Amps are awesome, but can be pricey and it's difficult to do a full budget system using them.
I fully recommend using Alpine headunits. I have had a couple of Alpine headunits, Kenwood excelons, Clarion, Panasonic, JVC, and had experiences with others and Alpine is clearly the best in my opinion. You can get a great deck for a decent price. I recommend getting at least this unit:
Alpine 9851 (there are some available for less, but if you want iPod integration this is the lowest Alpine that works with their iPod control, this is what we are putting in my truck): http://www.crutchfield.com/S-xg4011O...0&I=500CDA9851
Awesome price on a sub/amp package with MB Quart sub and amp, i mean, really awesome:
KnuKonceptz.com Amp Install Kit:
Alpine 9851: $279
Sub and Amp $299
Sub Enclosure: $89.99
Amp Install Kit: $31.99 (shipping is reasonable if not free from them)
=$700 + free shipping at Crutchfield and -$20 refer a friend discount (I can give you my code) = $680 (Another great thing about shopping at crutchfield is I believe they include the dash kit and wiring harness for free when you purchase a headunit from them)
That leaves you about $300 to play with, you can get door speakers and an amp to power those, or door speakers and iPod Interface and XM or sirius radio and run off of deck power or some other combination of the above.
If you want to keep it simple with the door speakers and go with something that goes in the factory location and run them off of deck power for now this is a good choice:
If you want something a bit nicer and aren't afraid of modifying the door panels for components and using speaker adapters you can get something like this and still have it be a budget buy (I just bought a pair for our truck)
Infinity Reference 6000cs:
Staying with the Budget theme, Infinity Reference 7520a 2 channel amp:
Infinity Reference 6000cs - $112.95
Infinity Reference 7520a - $99.95
KnuKonceptz Amp kit: $31.99 (alternatively if you get the amp kit you can get a wiring block and another 2 channel cable from knu konceptz)
So add the two together: $680+$250 = $930
You have a rocking complete system for $930 with $70 leftover or add ipod control or satellite radio.
Just one scenario, everything will have full factory warranty, and you get service you can rely on.