What is a cover, exactly? Where does the line go? There are blue and jazz standards, overlapping with Great American Songbook concept, that aren't really called "covers." Traditional songs (you know, Scarborough Fair, Greensleeves, Child Ballads etc.) aren't covers, either. Neither are arrangements and performances of classical music. The idea of "originality" or that certain songs "belong" to certain performers really only applies to popular music from the 50s on or so.
Happy Birthday, for instance, is a traditional song.
I don't think it's possible to name the most-covered song unless you restrict it to published recordings. We have no way of knowing about live performances. Even then, is a YouTube bedroom recording equal to a major label release?
I looked up a few lists (which did not explain their method or sources, though), and it seems Yesterday, Eleanor Rigby, Cry Me a River, Imagine, Satisfaction, Hallelujah, Summertime, Somewhere Over the Rainbow (if you accept these two under modern "covers") frequently appear.
I am less interested in the absolute number of covers than in their variety, quality and success, though. It would be cool if you could link to the relevant covers of the songs you suggest so we get to hear them.