Here's what I normally recommend for someone who doesn't want to blow the budget up. Start off with a new CD head unit, something with sub level controls and at least dual RCA out, 3 is better. I'd say around 150$ would get you something basic that works and will even play your Ipod, but you can always spend more here depending on your desires. Assuming all of your stock speakers are working we'd normally leave the rears stock for now. Swap out the front with a nice basic component set, 150$-200$ can get you into something that sounds nice and doesn't require a ton of power to work. Now we're to the sub section. Depending on the space you can give up a single or dual 12" box is going to be nice. If you want to keep some space I recommend a single 12 of a little better quality. I'd budget around 200 for that. Then we need an amp. If you're content with your system at this level we drop in a 250-500 watt sub amp at 150-200$ and call it a day. If you think down the road you want to go to the next level we put in a 4 channel amp, run the front speakers from the front channel and bridge the sub on the rear channel. This is going to give you great quality and some nice bass. Down the road then you come back and we drop in new rear speakers and move the amp to running the 4 interior speakers, and we add a subwoofer amp. Now you've got even more clarity and volume inside with more power on the sub for added thump.
Even the basic setup is going to be over your budget a bit, but sometimes it's worth a few extra bucks to get to the right quality level. You can certainly just add a little bass if the clarity is acceptable for well under 500, then move onto the highs later.

 

+1 Luke. Well put...

Have you shopped around yet to come up with anything you like? I actually had a member from TR call me yesterday quoting this thread for some pricing. I thought it was you but he just said he was in the exact same scenario. We basically put together exactly what luke81 just suggested with a closeout JVC H/U, JL Audio Evolution TR 6.5" front components, left factory rear 6X9's, closeout Kicker 12" CVR in a vented prefab box, and a closeout US Amps Xterminator 1600.1. All parts and labor was $745. Any shop here should be able to do something similar to this for you in this price range. Very common setup as you can see.

If you want to hear what this sounds like, his car will be done on Friday by 4pm or so. Not the same model as yours but it will be setup almost identical. Although he bought the last of many closeout pieces we had, there is allot of stuff out there that will still get you out for around $750.