If we are talking motorcycle engines then the Honda C50 would go to the top of the list. Also now excessively cloned by the Chinese, this little engine just runs and runs with no problems. Maybe not seen as much in the US, it is everywhere in the rest of the world. (I had one for 7 years, given to me, hardly any problems) Compared to engines of larger size, it's bearings, camshaft, gearbox gears etc would be extremely large. A good little engine, still in use today.
The BMW Airhead (1969 - 1996) is also considered very reliable, and although it isn't really, I guess it's just a comparison to other motorcycle engines.