@EvelineClariss Iroha/Sana, Momoko/Mitama, Rena/Kaede, and Alina/Karin are also also popular pairings. There's also ships with smaller followings like Hinano/Emiri and Konoha/Hazuki.
@Veya I somewhat agree with you about your Mami/Nagisa thoughts although in the Madoka universe where young (magical) girls have to frequently fight monsters (Witches/Dopels, familiars, rumors, demons...) them forming (romantic) relationships with each other does seem helpful especially considering what can happen if too much "negative energy" builds up.