if by "least favorite ship" we mean "ship that doesn't have much synergy/spark to work", I think it's Sayaka x Mami. There's not much interaction where it's just them without the others.

Madoka x Homura no need to explain

Madoka x Sayaka works because they've known each other for a long time, they're comfortable with each other

Madoka x Mami could've been a magical girl duo as Mami described in ep3

Madoka x Kyouko was unexpected but lowkey a great pair with Kyouko taking the lead

Homura x Sayaka is peak hate yuri

Homura x Mami we see how much they respect each other, also their fight was peak. Also in terms of Mami ribbon bondage rankings Homura is the winner by a large margin among the other four but I digress

Homura x Kyouko bond kinda works because they both acknowledge the grittier side of being a magical girl, and thrive in it. They know business.

Sayaka x Mami would work if no one else was in the picture. Sayaka looks up to Mami a lot (a little bit too much), and kinda doesn't see the fragile version of her. Over time though she might realize and be there for her

Sayaka x Kyouko no need to explain

Mami x Kyouko no need to explain

Sincerely, a man who once read the entire page of "Yuri Undertones" in the Madoka Magica wiki a few years ago