Eagle pay rates differ for the amount of seats in the back for captains.
The 140 has the same engines as the 135, but more weight. The resulting performance is lacking compared to the 135 and 145. But the landing gear on the 140 is better, and there is some talk about retrofitting 145s with it to help with the all too common empty weight restrictions.
The inside configuration differs too. The locations of some of the fire extinguishers, baggage locations, oxygen canisters, etc are swapped.
I prefer the 145, because I've never had a problem holding max speed in cruise, but the 140 has stuck us at .72 several times.