In general, it is more cost effective to get small bookshelf speakers and a subwoofer, than it is to get full range speakers. This is particularly true in the case of surround systems with 5 or more speakers. Just make sure your main speakers go low enough to keep the sound from being localized at the subwoofer; the THX standard is 80 hz, and I would advise getting bookshelf speakers that go at least that low.
Your budget is rather low for me to advise you, particularly if you want to buy more than just speakers with that $1000. Do you expect to get just speakers for that price, or will it include a receiver and other components?
If you are just wanting 2 channel speakers for about that price, I would recommend considering Magnepan MMG:
http://www.magnepan.com/model_MMG
And SVS PB10-NSD:
http://www.svsound.com/products-sub-box-10nsd.cfm
PROVIDED that both:
1) Your amplifier can deal with 4 ohm speakers; and
2) Your preamplifier has a line level subwoofer output.
Another speaker to consider is the Aurum Cantus Leisure 2SE:
http://www.kellsieavdesign.com/products/Leisure2SE.htm
This version of the speaker retails for $1499, but it has sometimes been sold on ebay by Kellsie for under $1000 (though I do not think they currently have any auctions for them; contact them if you wish to buy a pair). These are excellent speakers, and are an easy load for pretty much any amplifier.
I should warn you, if you buy Aurum Cantus Leisure 2SE speakers, there are at least 4 versions that have been made, and I have seen an auction on ebay in which the seller misrepresented which version he or she had for sale. In order of supposed quality are:
Leisure 2SE Signature (current U.S. version)
Leisure 2SE (original U.S. version)
Leisure 2SE (international version)
Leisure 2SE (Chinese version)
The Chinese version uses a regularly shaped cabinet, without sloping sides and front. And you can tell the international ("generic") version from the U.S. versions by:
http://www.kellsieavdesign.com/products/US_vs_CH.htm
I personally have owned both the international version and the original U.S. version. The frequency response of the U.S. versions is flatter and goes deeper by 5 hz than the international version. Also, the U.S. versions are slightly more efficient than the international version. All are good, from what I have been told (and from my experience), but I can say definitely that the original U.S. version is superior to the international version, both in looks and performance.
