If you're looking to spend less than $1000, you've got quite a wide palette of choices, and you shouldn't have any trouble getting a great guitar.
My personal favorite is Seagull. They make all of their stuff out of solid wood (no pressboard) in Quebec, and they make everything by hand. They've got a number of different lines, some of which are more expensive than others, but they're all excellent instruments. I would recommend something from their S-Line or their Artist line, both of which have guitars for under $1000. I have an S6+ with the cutaway, and I absolutely love it.
I've never played any of these guitars, so I can only go off of reputations. Martin, Taylor, and Gibson are all really good names and all have excellent reps as acoustic guitar manufacturers, although since I've never played one, I can't really offer any suggestions on specific models. Takamine has a decent rep, Ibanez is supposed to be good, and Washburn is a good name too. I've never played any of those either, though, so I can't help you much with any of those.
Ovations are pretty good, although I've got to say that I don't care for the way they sound unplugged. If you route it through an EQ pedal and an acoustic guitar amp or a PA system, it sounds really good, but the guitar sounds relatively quiet and kind of tone dead (IMO) compared to a conventional acoustic.
Sorry if I didn't help much with brand suggestions, but here are a few other pointers. Try to find a guitar that's not made in China, Korea, Japan, or Mexico--made in Canada is good, made in the USA is good too. Don't buy a guitar that's made out of a wood laminate or pressboard. Solid wood is always better, especially since they sound better with age.
Hope there were a few helpful tips in there. Good luck on your guitar!