Good question.
Rarity in itself can't count or basic Halfords specials from the 80's would win - in the same way that there's probably less Morris Marinas and Simcas left in the world than Ferrari GTOs.
So that also means that production bikes, however high end are out.
So is custom: any frame builder could do you a quirky special from nice materials.
Therefore it has to be down to significance, and I'd say this boils down to two fields -
Technical significance: innovative build methods, shapes, materials etc. These would be exemplified by prototypes and the likes.
Historic significance: actual bikes [frame as a minimum] that won a race, were ridden by champions, hold records, or have a fame value.
So taking a mixture of each field, the most super bike would be a famous protoype - probably one of the US westcoast testbeds that started it all off.
Any suggestions all you VRC types?