I believe the best value in a stick/throttle (HOTAS) setup is the Saitek X36 and X45 series. The X45 is the current version, retailing around $75. I got mine a while back w/ a $30 mail-in rebate I think.
Unfortunately, their software stinks from what I understand. It's so bad that 3rd parties have stepped in to write drivers & button-mappers. So there are a lot of downloadable mappings for all popular games out there. It's a pretty full-featured stick, and the build quality is good. Two main things I don't like are it's built for large hands, and there's a pinky <shift> button that while adds functionality, really is not ergonomic.
I can't really give more specific recommendations because I've never really invested the time to really get into a flight sim, even though I own quite a few titles. :/ If I weren't buying Saitek, I'd probably go with CH. They have a long, successful track record as well.