The American Eagle branded airlines (Piedmont, PSA and Envoy Air) are wholly owned by American Airlines and offer flow through agreements to their parent company. Although, I hear that it can take some time before you flow through.
United recently purchased a large stake in CommutAir (which is slated to grow by 300% over the next few years). Concurrently with this they announced a Career Pathway Program (CPP), which allows you to chance to interview directly with United Airlines. I f accepted into the CPP program, once you meet the qualifications you will be placed into the pool of candidates awaiting a class date (So it's not a true flow through agreement per se, but you will upgrade to captain much much faster than at the American branded regionals).
ExpressJet also just recently announced a CPP program with United, although that airline is shrinking, and the CPP was probably a way to slow the attrition.
Full disclosure, I am a pilot with CommutAir.
Better info can be had at the well known US Airline forum regarding these airlines.