I'm starting with the age category and genre most near and dear to my heart, MG Speculative Fiction.
Kat Stephenson from the Kat Incorrigible by Stephanie Burgis: Kat loves her family and is fierce about protecting them all even when they don't appreciate it.
Fer from Winterling by Sarah Prineas: She is a heroine who saves her people and land. She is a leader who makes some hard mistakes and does the harder work of atoning for them.
Alunna and Callie from Above World by Jenn Reese: Both of these girls are leaders. They have different strengths, but together they make a great team.
Zita from Zita the Space Girl: She is fierce, smart, and sacrificing.
Neverfell from A Face Like Glass by Frances Hardinge: Neverfell is trusting and kind and good in every way imaginable. And she's a true hero.
The MG SFF heroines that were in the original post who you can read more about here:
Kate Sutton from The Perilous Gard
Meg Murry from A Wrinkle in Time
Hermione Granger from Harry Potter Series
Millie Chant from the Chrestomanci Chronicles
Aravis Tarkheena from The Horse and His Boy
Do you have any favorite MG Speculative Fiction heroines?