People who like Samus are sexist. If you were surprised that she was female fair enough; if you were surprised because, I quote, "I was completely surprised and ignorant at the time that a female character could make that great of a game." then... well, that itself explains it. These days she's just a poor excuse for a slut.

People only like Croft for boobs; as a character she's horrible.

Shepard can be male or female, so doesn't count.

Zelda is kind of applicable on account of Sheik, but that doesn't make her one of the best at all.

Claire and Jill work, though.

"I think it comes down to this, most male gamers won’t admit they enjoy playing as a strong female character who can hold her own." I disagree. Nariko, for example, is one of my absolute favourite protagonists of any game, and she damn sure deserved to be on that list more than most of who you chose (if you're willing to forgive the fact Heavenly Sword was a bad game). And passing up on The Boss but including Zelda is ridiculous. And even considering Peach is also ridiculous.

Refer to this.

Claire and Jill are definitely at the top of the list of female characters. oh, cant forget Ada. RE games have awesome female characters.