Here's a picture that illustrates the square hole and the round hole on the right hand side of the engine.
Square Hole
As BakerBoy stated in his post above, the square hole is a drain for any liquids that might accumulated on the top
outside of the engine, up between the 'V' of the cylinders. Today, I took the Tupperware off my motorcycle and thoroughly washed the engine... after starting the moto, I was horrified to see pure, clean water coming out of the square hole - you can see the rivulet of water in the photo below.
After reading the above discussion, now I know that it was nothing to worry about - the water I saw draining out of the square hole came from the garden hose I used to wash down the engine, and it was draining out the square hole from the 'V' up between the cylinders, exactly like Honda intended it to do.
Round Hole (Round 'Pipe with small hose' from 2008 onwards)
Again, as BakerBoy explained, the round hole is where coolant or oil that leaks through the waterpump seals will escape from. The engine pictured is a 2012 ST 1300, hence it has a little metal elbow stuck in the hole, with a drain hose attached. The drain hose exits at the very front of the engine, at the bottom of the motorcycle.
If you want to know how the water manages to get from the V between the cylinders down to this square hole, have a look at the picture in post #5 of this discussion:
Coolant Leaking Again.
Michael