You can't really cross-compare between 2 totally different aircraft because it really depends on the route. I'm not sure which aircraft burns the least fuel/hr, but as far as making money, there are a whole lot of variables to consider. Distance and demand come to mind first. MEM-PIB (Pine Belt) used to always be on a Saab 340. I don't know about the loads then, but now that we are doing it on a CRJ-200 I haven't seen anything close to a full plane. Not saying it doesn't happen from time to time, but in general that route is much better suited to a turboprop than a jet. Delta apparently doesn't care though and is willing to waste money throwing a CRJ-200 down there 2-3 times a day.

On the flip side MEM-ICT (which I think we no longer do) is way too long of a flight for a prop, but we were usually full on the -200. Pretty solid bet that it at least broke even most of the time. Some short routes are always full and have lots of high fare business passengers (GSP-ATL comes to mind) so putting a larger regional jet or even a mainline aircraft many times makes sense.

Now comparing different airplanes of similar characteristics is a different story. I don't really know whether a Saab or a Dash is better on a given route, or a CRJ/ERJ either. I've heard the CRJ is better, but I don't have numbers to back that up.