I'm building a 5.1 home theater for my great room/living room.  The room is just so big we need the extra power to hear anything on the TV.  

The receive will be a Marantz 5009.  I'm looking for a 5.1 speaker system similar to the Bose systems that have the smaller speakers.  The room is pre-wired for 5.1 in the ceiling, I just need to buy speakers and mount them.  Because it is the great room and not a dedicated theater room, I'd like smaller speakers that do not dominate the room.  Anyone have any suggestions?  Price no more than $1000.

You could always do in wall speakers if you don't want to see them. Id go that route before I went super small. You cant go with small speakers and have it not affect the sound quality.

Get on the forums at audioholics.com. You will be asked the volume (not area) of your room and if it's open to other rooms (probably go with a ported sub if so). I don't have any recommendations for you other than "cry once - buy once."  Maybe Hsu Research has something good in that price range that fits. If I weren't at the pub, then I would do a search.