The ‘parents guide’ section of any given movie on IMDb tells you what to look out for in these films. My kid saw these but not all can.
Boy (a New Zealand film)
Sci-Fi
Gattaca
Artificial Intelligence
I, Robot
Horror
Anime to watch while you’re still a kid
Princess Mononoke
The Girl Who Leapt Through Time
Wolf Children
Wolf Children and Grave of the Fireflies are also great but the latter in particular is very sad. Wolf Children is probably more sad for adults than for kids.
Kickass older teenage girls
Whip It!
We Are The Best! (Swedish, and hard to find)
Films for adults which a 12-year-old would probably understand
True Grit (either the old or the new one, but the dialogue in the old one is easier to understand)
Talullah
What Maisie Knew
Boyhood (it’s long, needs an intermission)
Mud
Panic Room
Flightplan
Gritty but good for discussion:
Into The Wild
Samson and Delilah