This would require a search on the most commonly used videos sites, so the answer to this question will not be accurate. The most covered songs seem to be which ever gets the most views.
The list below appear to be the most commonly covered songs by other Vocaloid, UTAU, Nico Nico and YouTube singers. They have also been translated and sung in various languages. It is "Miku Miku ni Shite Ageru" which continues to be treated as a kind of anthem for Miku and for Vocaloid, the song has been dubbed in various languages, parodied, and rewritten.
- Black Rock Shooter
- Miku Miku ni Shite Ageru