First if you want the best advice I would post your question on a Home Audio Speaker forum. You will get much better responses, with more information. http://www.avsforum.com/forum/89-speakers/
For no more than $1,000 I like this set-up
-Pair of Pioneer SP-F52-LR towers, $127/each shipped (http://www.amazon.com/gp/product/B008NCD2S4/ref=ox_sc_act_title_3?ie=UTF8&psc=1&smid=ATVPDKIKX0DER)
-Pioneer SP-C22 Center Channel, $97 shipped (http://www.amazon.com/gp/product/B008NCD2EI/ref=ox_sc_act_title_1?ie=UTF8&psc=1&smid=ATVPDKIKX0DER)
-Pioneer SP-BS22-LR Book Shelf speakers, $127/pair shipped (http://www.amazon.com/gp/product/B008NCD2LG/ref=ox_sc_act_title_2?ie=UTF8&psc=1&smid=ATVPDKIKX0DER)
-NXG Technology NX-BAS-500 12" 500-watt Powered Subwoofer, $270 shipped (http://www.amazon.com/NXG-Technology-NX-BAS-500-500-watt-Subwoofer/dp/B008FSTU4G/ref=lh_ni_t?ie=UTF8&psc=1&smid=A28SS3BS1DBQ92)
-Denon Factory Refurbished AVR-E400, $250 shipped (http://www.accessories4less.com/make-a-store/item/denavre400/denon-avr-e400-7.1-4k-3d-networking-receiver-airplay/1.html)
Now I will not deny Mel H posted a great setup with the exception of the receiver he recommended. Yamaha receiver are very over priced and struggle to make the power they claim to put out when they are tested. HSU is a great subwoofer company but that is a whole chunck of your budget when this being your first subwoofer you may not notice the benefits of it. Plus the NXG is very well rated subwoofer by Sound&Vision Magazine (http://www.soundandvision.com/content/review-nxg-nx-bas-500-subwoofer ) with very surprising output numbers for its cost. I like the HSU products but I save them for people with $500+ alone to spend on a subwoofer. Same goes with SVS. Unfortunately neither HSU or SVS fit in your budget. Besides if you wanted to blow either of those out of the water the best subwoofer for $500 shipped right now is the Outlaw LFM-1 Plus. (Its has much more output than the HSU STF-2 and offers variable port tuning so you can configure it to hit the low deep bass, or offer maximum output which will give you louder bass just not as low. The Outlaw is meant to go head to head with the HSU VTF-2)
If you want just a stereo setup to start off with under $1000, here is what I like
-Polk RTi6's Bookshelfs, $200 shipped (http://www.ebay.com/itm/Polk-Audio-RTi6-BLACK-Bookshelf-Speakers-NEW-PAIR-/390813524204?pt=Speakers_Subwoofers&hash=item5afe4d20ec)
-Outlaw LFM-1 Plus Subwoofer, $500 shipped, sale price (http://outlawaudio.com/products/lfm1plus.html)
-Denon Factory Refurbished AVR-e300, $190 shipped (http://www.accessories4less.com/make-a-store/item/denavre300/denon-avr-e300-5.1-3d-networking-receiver-airplay/1.html)
There is NO need for towers if you are using a good subwoofer like comes from Outlaw, HSU, and SVS.
With a pair of speakers you miss out on surround sound. Stereo is great for music but once you go surrounds sound you rarely go back.
Check out the audio forum I linked I bet they will agree with my set-up if you want surround sound and Melv H's if stereo is enough for you.