In no particular order.
Balsa From Seirei No Moribito. A very rare instance of a strong tastefully done female main character in an anime.
Toph Beifong from Avatar. She's the most badass character in the entire series... and she's a blind little twelve year old girl.
Rogue from X-Men, I've always loved her character. Her powers are incredibly useful, but at the same time they're a horrible burden. I'm looking forward to her being in the new Avengers comic that's coming up soon.
Tali'Zorah from the Mass Effect series. She's intelligent, but she can be pretty airheaded at times(which can make her adorable). She was also one of the more interesting female love interests in the Mass Effect trilogy.
Arya Stark from Game of Thrones. Kind of like Toph, she's one of the most badass characters in the show. She's a really smart kid too, and I loved her conversations with Tywin in season 2. She's very tough and vengeful as well... that's one little kid I wouldn't want to piss off.
Mrs. Brisby from The Secret of NIMH. She was pretty much the first heroine I had ever been exposed to as a kid, and I loved her. She was scared quite a lot throughout the movie, but when she had to be strong, she could be strong.
Celes Chere from Final Fantasy VI. I liked her character, and her relationship with Locke(who is my favorite character in the game} but the opera is where she really became one of my absolute favorite characters in the game.
I think I'm just going to stop there. I could keep going for a while, but the post would be just too long.
Balsa From Seirei No Moribito. A very rare instance of a strong tastefully done female main character in an anime.

Toph Beifong from Avatar. She's the most badass character in the entire series... and she's a blind little twelve year old girl.

Rogue from X-Men, I've always loved her character. Her powers are incredibly useful, but at the same time they're a horrible burden. I'm looking forward to her being in the new Avengers comic that's coming up soon.

Tali'Zorah from the Mass Effect series. She's intelligent, but she can be pretty airheaded at times(which can make her adorable). She was also one of the more interesting female love interests in the Mass Effect trilogy.

Arya Stark from Game of Thrones. Kind of like Toph, she's one of the most badass characters in the show. She's a really smart kid too, and I loved her conversations with Tywin in season 2. She's very tough and vengeful as well... that's one little kid I wouldn't want to piss off.

Mrs. Brisby from The Secret of NIMH. She was pretty much the first heroine I had ever been exposed to as a kid, and I loved her. She was scared quite a lot throughout the movie, but when she had to be strong, she could be strong.

Celes Chere from Final Fantasy VI. I liked her character, and her relationship with Locke(who is my favorite character in the game} but the opera is where she really became one of my absolute favorite characters in the game.

I think I'm just going to stop there. I could keep going for a while, but the post would be just too long.