Kamina from Gurren Lagann
Spike from Cowboy Bebop (even though it was part of the greatest ending of all time)
Boss from MGS3
But the first one that came to mind for me was Emma Sheen from Gundam Z, which really made me pretty depressed and angry. She was the 'normal' person hero of the series, no newtype powers to speak of and really nothing special as a pilot but she was still a strong character. The spectacle of the whole situation didn't help. An entire battleship is sacrificed trying to save her and then she still dies, in severe pain, in the main character's arms.