Right now, I'm fond of those all-Alco regionals in Pennsylvania and New York, as well as the Missouri & Arkansas.
My lifetime favorite has long been a fallen flag -- Pacific Electric, as I lived near their track and they had many endearing quirks, such as Baldwin VO-1000 switchers with trolley poles mounted on the hood to activate crossing signals when operating under trolley wire. And they also used every variety of Magnetic Flagman wig-wag crossing signals, including some unique to PE -- many mounted on the wood catenary pole close to a crossing, and one suspended from wires like a traffic signal. Who couldn't like the PE?