I will give it a rough start. I know I am forgetting a lot.

American:
AA Eagle
Trans States

United:
Skywest
Chataqua/ Shuttle America
Trans States/ GoJet

Delta:
Skywest/ASA
Comair
Chataqua/ Shuttle America

Northwest:
Mesaba
Pinnacle

Continental:
Expressjet
Chataqua (now or soon)

US Air:
Air Wisconsin
Chataqua/ Republic
Piedmont
Mesa
PSA
Trans States

Alaska:
Horizon


Anyone care to add. I filled in all the big regionals (Skywest, Eagle, Mesa, Comair, Trans States, Horizon, Air Wisconsin, Expressjet, Chataqua...) What is this missing?