From what I've read, the Onkyo 506 is a good unit and should serve you quite well for a computer system (or an entry-level HT). The Dayton sub gets good reviews here, and the customer reviews at Parts Express are also very good.
So, that's roughly $204 (Onkyo) + $155 (Dayton) + shipping on the Dayton. Just FYI, shipping on the Dayton can be as high as $40.
If you're ignoring shipping in your budget, the you have $700 - $204 - $155 = $341 for speakers. I honestly don't know what I'd get in that price range. The Ascends that Mazer suggested have gotten some good reviews (that's my memory of those), as have several others in that price range. You have many options in that price bracket, ranging from internet-direct to main brands that you can buy locally or off the internet. My strong recommendation is to buy from someplace that will let you return them if you don't like them, preferably without a restocking fee or high shipping fees.
EDIT: I see that you're considering $1000 total. That gives you even more options (of course
).