Nose shape and brow ridges... eyebrows are also super useful.

Do you know I never wondered what made me recognize people's faces. I do rarely mix manga characters around though. So maybe the hair?? :}

Do you have trouble when people change their hairstyles, then?

I have SO much trouble when people change their hairstyle in mangas!
I remember reading one where one characteristic of the protagonist was different hairstyles every day. Each time I wondered if it is her or somebody new

Yeah, I definitely need help.
Especially when you read ones where they have personality switching, or get possessed by a ghost, or dress up as someone else, or something like that.
I can't do it! I can't keep them straight when that happens! If I own the books and that happens I always end up actually taking a pencil and labeling the characters because it's useless to even try and figure out what's going on without it....

Yeah, the characters changing hairstyles can really throw me off if the rest of the character looks generic.
One of my favorite manga's right now is Skip Beat. It's about acting and sometimes i have the hardest time recognizing some character because their hairstyle changed. But the Protagonist changes her style for every role/audition and I can recognize her easily as the artist put in the effort to make her her own person. :}

I think I've heard of Skip Beat :)
It is also easier if the manga is in colour, not only black and white.

Mmm, at least the characters seem to often call each other by name, which is about the only reason I don't get entirely lost.

fruits basket have a lot of different characters so I can generally tell who is who

True, FB was one of the few back then that had a big diversity in characters. Plus all of them reminded people of the animal they were. :}