Stay away from Mesa and GoJets. There is no valid reason to be a newhire at either of these carriers. Mesa is a pox upon the industry, dragging down eveyone else. GoJets is an alter ego airline. Working there makes you the next best thing to a Scab. (Note the difference - Mesa crewmembers are all good guys getting a bum deal from the worst Airline CEO since Lorenzo. GoJet crewmembres are buddyFokkers.)
Xjet, Eagle, SkyWest, Republic Group, Air Wisconsin, Comair, & Horizon are probably the top tier. These are places you'd likely spend your entire regional career at happily.
The balance of the carriers listed at
http://www.airlinepilotcentral.info/.../regional.html
are places that are either stepping stones to another regional, or places that might be a good fit for your specific circumstance.
I flew for PSA. Had I been from Charlotte, or if I had been able to move there, I probably whould have stayed. Despite the long upgrade, long reserve, and poor schedules, if I didn't have to commute it would have been tolearable.
CommuteAir, Colgan, Great Lakes, all have poor pay and work rules. TSA doesn't put you in a hotel for training. Pinacle and Mesaba just got thier contracts raped by a bankruptcy judge. But if one of these is your home town airline, it may be in your best intrest to fly for one of them. Or if one of them hires you 500 hours earlier than any of the better regionals, go there; but don't be afraid to quit after you get enough time for a better gig. Watch out for airlines with a training contract. If you have to sign a contract to stay, then they must have a retention problem; and that is usually caused by poor Quality of Life (QOL) issues: ie Pay, Schedules, Work Rules, etc.
Read these boards. Places people b!tch about are places to avoid. They brag about placed thy're happy at. You won;t take too long to figure out which is which. If you have a question about life at a particular company you're leaning towards, ask. People will come out of the woodwork to answer.