I have owned most of those and like the three cylinder yamaha the best.
The merc classic 50 in the later years (1986 on) was rated at 40hp and as a four cylinder it has four tiny pistons and an idle that rivals a four stroke. The motor will run with any modern day 40/50 and spank any 50hp four stroke. Weak areas are the lower motor mounts wear and the outer water jacket can pinhole when used in salt. No removeable cylinder head. Early models have the annoying cowl wrap that means three pieces need to come off to access the motor. Later models have a better lower unit and a nice lightweight one piece cowl. Oil injection if equipped is a pretty reliable system, oil tank under the cowl and gravity fed. This motor will be a crossflow generally crossflows idle better than loopers. Later models will have a better trim system too, either a trouble free gas assist or the power trim mounted between the C brackets.
The OMC two cylinder is a tough little bugger but cannot run or idle as smoothly as the Merc classic and Yamaha threes. Hard to beat a big twin though, reliable and tough. Agree with Spare on the lower units the seems the 1990's 50's had a weaker foot than the earlier ones. VRO equipped models have the external tank and a lot of controversy about the system's reliablity. Most will be converted back to a premix.
I have had a bunch of three cylinder yamahas and like them the best. Compared to the three cylinder OMC's (the original loop charged engine) the Yamaha is just more refined. Something about the sound signature of the Yamaha appeals to me and the idle quality is much better than the OMC 60/70hp. Oil injection is the brightest of the three as the oil is injected behind the carbs, less chance of failure. Yamaha parts are more expensive but the electronics seem to last better than the merc and OMC. Early Yamahas used a mild steel shift linkage and the sterering tiller arms are prone to rust when used in salt. Shift shaft will stainless after early 1990's. These are loopers and at higher rpms when the exhaust scavenging kicks in it is much like opening the secondaries of a 4 barrel quadrajet...cool. Early 80's Yamahas have sucky paint and graphics that will fade away quickly later models are much better.
I haven't much experience with the three cylinder mercs so I won't comment.
You really could not go wrong with any of them as long as you get a well cared for engine.
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