I personally thought ending A should have been the real ending, although I did also like B.
Ending A
Ending A probably has the least amount of plotholes, but ending C is more interesting. Ending B made the least sense and wasn't very well explained.
I just noticed when watching it just now that Mrs. Peacock is not in the Billiard Room with everyone else after Yvette screams.
Also Colonel Mustard did leave Miss Scarlet when she suggested there was someone behind the curtains in the ballroom.
Ending C, because the punchline is fantastic.