Although everything, including pairings, in Vocaloid is purely fanon, the most popular heterosexual ships seem to be Gackupo/Luka, Kaito/Miku, and Len/Rin.
Miku/Luka is the most popular homosexual pairing, having had albums full of songs about their love. Yaoi fans, however, tend to gravitate towards Kaito/Gakupo.
In the album In the Aeroplane Over the Sea by band Neutral Milk Hotel the narrator often alludes to Anne Frank. Fan interpretations include the pairing of Jeff Mangum, the writer and singer of the album, with Anne Frank and the belief that Jeff actually is in love with her. The lyrics, many of them sexual in nature, seem to be the main reason people come to this conclusion.