The least POPULAR Vocaloid is Ryuuto, mascot of Gachapoid, produced by Internet Co., ltd.
To add to this, Tone Rion by MOEJapan seems to be rivaling his unpopularity. Also the most unpopular English VOCALOID is Tonio (which is probably used less than Tone Rion + Ryuto). Clara and Bruno are in a similair boat while SeeU is unpopular in the Japanese market but one of the more popular in the overseas. Also, Mew has not hit off particular welll either.
Populairty, however, does not nessecary reflect sales.