I like Athearn, Atlas, and Kato.
Each manufacturer has their pros and cons.
I like Athearn RTR since the models are decently detailed for the price, and the drive is easy to disassemble and clean. There is also ample room inside to add speakers for sound. The drive, however, can be a hit or miss.
With Athearn Genesis, I like how they have ditch lights as appropriate to the prototype, but with some of the models, the motor leaves a lot to be desired. Also, Athearn messed up quite a bit in the Genesis line, basically quality control problems, but generally I would not hesitate to buy an Athearn Genesis engine.
I also have quite a few Atlas engines. They are nice and smooth and relatively quiet although they don't like to add ditch lights to anything except widecab GE diesels.
As with Bachmann.... Lets just say that I haven't met a Bachmann that I've liked, in any of their lines.
BLI engines are heavy and run great, but I'm not a huge fan of the sound (I'm spoiled by being around the prototype very often). The SD40-2s are similar to the Kato shell with finely molded fans that aren't see-through.
I don't have any Intermountain engines so I can't comment on them. They haven't made anything that fit my era (yet).
Kato engines are the smoothese running by far, but some models such as the early SD40-2 have a really weird pickup system. The shells have finely molded fans that are not see-thru, and the handrails are fat and not scale. The details aren't up to today's standards, but the drives are the best in the industry.
MTH - Lets not go there.
Walthers - The trainline locos aren't the best detail-wise, but have a smooth drivetrain.