Big Zappa fan that I am, I'm still dubious as to what 'song' of his you could put in a top 50.
An actual song with lyrics, eliminates the vast majority of his work as a sizeable amount of his songs with lyrics would be questionable to a critical mass audience, required to get a wide enough appeal.
Being subjective as well as looking for a wider appeal I'd put
Peaches en Regalia high up the list (Instrumental though)
Bad News Coming Every Day. A good shout.
Being purely subjective I'd have Watermelons in Summer Hay in the top 10.