I think the title of this thread speaks for itself, so I'll just list the ones I know off the top of my head.
Late for school. Bonus points if they have a slice of toast hanging from their mouth.
Dreaming of things to come. Or in the case of Madoka, dreaming of things that passed.
Second episode starting with the main character dreaming of the events of the previous episode, then waking up and wondering if it was a dream before finding obvious proof that it wasn't. Otogi-Jushi Akazukin did this before Madoka Magica.
The Mysterious transfer student. Bonus points if that character appeared in the above dream.
The main character/s being chosen by destiny. That's pretty much why Lila doesn't believe Altarie. She thinks that Magical Girls are born into the role through destiny and doesn't think consider the idea that they'd be causally picked just because, or given the choice.
Pigtails. Hairstyle of champions. They symbolize childishness and innocence, so it's understandable that an ungodly amount of Magical Girls have them.
Stuffed animals. Girls love them and Magical Girls are no exception. Bonus points if their rooms are littered with them.
Same goes for sweets.
Just wants to be normal. In the old days a Magical Girl just wanted to hang out with her friends and have fun, and didn't care for the burden of fighting monsters and saving the world. I blame a certain White Devil for the recent surge of "I just wanna be special" Magical Girl protagonists.
Character inserts themselves into a normal, human family. Minky Momo did it way before Chibiusa. The fact that they look similar makes me wonder if that's not a coincidence.
BRAINWASH SOMEONE OTHER THAN THE LOVE INTEREST!