I know eagle used to deny jumpseat/non-rev benefits to new hires for six months. And they required you to live in San Juan, PR. Not sure what their policy is today, but that was only a couple years ago.

Other than that, I think most of your large regionals are ok with commuting since LOTS of folks do it. A lot of it depends on the city pairs in question. If you have several daily non-stops on your company or codeshare, then you're in great shape. I did coast-to-coast for while; it sucked but was mangeable because I had the company non-stops.

Horror story: I knew a guy who lived in small-townville pacific northwest and flew turboprops out of hickville, new england. His commute:
Horizon to SEA, Alaska to LAX, USAir to Philly, Company bird to his domicile. Nightmare....