Besides the very unpopular Atraxa, praetor's voice (/s), I love my heartless hidetsugu deck. Commander burn is ... somewhat viable but delicious. Maddening hex, thermo-alchemist, guttersnipe, storm cards. It's all there!

Evra, Halcyon Witness is so much fun!

I don't know if he's considered unpopular, but Chainer, Nightmare Adept is one of my all time favorite commanders, when he is leading rakdos dragons. Every card is a dragon, mentions dragons, or has dragons in the art. It is so slow and clunky, but I just love it. The main goal is to get Bladewing, The Risen onto the battlefield from the yard to cheat another dragon into play, to then bring Bladewing's Thrall back from the dead. It's stupid and not powerful, but it makes me feel warm and fuzzy inside.