Its up to you
That is, unfortunately, a subjective question.
Everyone's paradigm has changed over the last five years or so. For example, in 1999 most everyone aspired to a career at United, Delta, or other major airlines. Jetblue, on the other hand, sounded like the name for a new mouthwash.
Today most pilots who are looking for greener pastures are more likely to talk about AirTran, Jetblue, Frontier, etc.
Regional airlines are no different. How "good" or "bad" one regional is when compared to another has quite a bit to do with what
you are looking for in an airline.
For example, if you're looking for a quick upgrade, a variety of domiciles, and a mix of codeshares, perhaps Chautauqua is the right choice for you.
If you're looking for a large company with a nationwide route-network, a good contract with good work rules -- but where the upgrade times might take a little longer (ok...maybe a LOT longer), perhaps Horizon or Comair might be more your speed.
If you're looking to fly some interesting equipment into small, challenging airports throughout the country but are not terribly concerned about working conditions or pay, perhaps Great Lakes or Colgan would interest you.
If you're a flight instructor looking to build experience before applying at a carrier that operated regional-jets, then a night freight operation such as AirNet, Flight Express, or even Mountain Air Cargo might suit you.
In reality though the decision will likely be made for you. Unfortunately it is a seller's market. Although there are still many airlines hiring there has never before been so many highly qualified pilots in the job market. With a little luck you might be able to target an airline with a domicile in the city where you would like to live -- but more likely, you'll simply apply to every airline and go with the first one who calls.
Good luck. Coming back to the "regionals" is a wake-up call, there is no doubt about that. But after a year or so you'll find that you barely remember what life was like before (save a ghostly memory of a larger paycheck).
Take care!