I recently went through this, and kept my focus primarily on bookshelf speakers because they're easier to deal with at this point in my life (graduate student). My focus was on only 2 channel music playback, I have a simple home theater in the living room.
There's a ton you should check out but I wound up with Totem Rainmakers. I also really liked Focal (check out the 806V and 807V, or the 706V, $800, $1000 and $600 respectively).
Others: Triangle Comete ES, Paradigm Studio 20 or whatever else they make (not a huge fan), B&W CM1 and 600 series (also not a huge fan), PSB is also very good. That's all I can come up with right now that I've had experience with. I would also recommend Axiom as an owner of a pair of their speakers. Of all the speakers I mentioned I really like Focal and that would be on my list for home theater use, but I don't think you'll get a floorstander from them for $1000. Axiom would probably be my pick for an affordable home theater, particularly if I wanted floorstanders for mains as they're not terribly expensive and I prefer a brighter speaker for home theater.