Quotes: Samus is a Girl

Must restore peace! Must escape! Peace in the universe is once again restored! HOLYCRAPIMAGIRL!!!
Brentalfloss, "Metroid in 10 Seconds"

Oh no, please don't tell me I've been slaying hot chicks this entire time.
Eddie Riggs, after one of the evil druids he was about to kill turned out to be an ally, Brütal Legend

Tony Stark: Good God, you're a woman! I honestly- I couldn't have called that. I mean, I would apologize, but isn't that what we're going for here? I thought of you as a soldier first.
Ramirez: I'm an airman.
Tony Stark: Well, you have actually excellent bone structure there. I'm kinda having a hard time not looking at you now. Is that weird?

Luigi: It's not fair, Link. The only people who flirt with me are other guys.
Link: Listen, if this is about that incident in '93, it was a really awkward time for me and I didn't—
Luigi: No. This bounty hunter guy tried to pick me up at the bar last night. Said he was only planetside for the evening and wanted to show me the time of my life. Couldn't even see his face under all that orange armor...
Link: Wait... Did this "guy" give you his name?
Luigi: Yeah. Began with a 'S'. Sam... or something.
Link: Samus?
Luigi: That's it! I told him I didn't swing that way...
Link: (facepalming) Oh, by Ganon's pork fetish, Luigi...
Luigi: What? What is it?
Link: Nothing. Not a gosh-darn thing. Say! You wanna come over and cry yourself to sleep on my couch for no reason whatsoever!?

"No, Sir."
"That's 'No, Ma'am'"
"No, M... Wait, you're a woman?"

Neo: I just thought you were a guy.
Trinity: Most guys do.

My first great triumph against impossible odds brought me a lot of attention. I think my favorite part of the whole affair was revealing to the waiting dignitaries who I am under my suit... The phrase of the day was "He's a whaaa?"

Hold on, the Assassin is a chick? How did I miss that?
The Assault, Monday Night Combat

Wasn't expecting me to be a woman, were you?
Samus Aran to Mario, Paper Mario X, Prologue: How to Steal a Castle

Whoa! Sorry about you suit... mam?! GUYS! We've been chased by a girl!
Sonic the Hedgehog, right after finding out Samus's gender, Paper Mario X, Chapter 61: The Mixed-Up Paths of Bowser's Castle

Gloomtail: WHAAAAATTT? You destroyed my precious younger sister!
Link: Hooktail WAS a girl!
Flurrie: Wait, you're Hooktail's brother?
Kirby: But what if "he" is a girl too...
Flurrie: No, I'm sure this guy's a... guy...
Paper Mario X 2, Chapter 72: The Tail of Gloom and Its Doom

Akira: Brother, you're alive!
Daigo: I'm sorry, Akira. It must have been tough for a lady like yourself...
Edge: What? His voice... it sounds like...!
Gan: A lady like yourself?!
Akira: I'm sorry I've been deceiving you. I'm not the younger brother of the big boss... I'm his younger sister...
Rival Schools: United By Fate

Sgt. Hondo Harrelson: Sorry, wrong room.
Officer Chris Sanchez: Who were you looking for?
Hondo: Chris Sanchez.
Sanchez: I'm Chris Sanchez.
Hondo: You're Chris Sanchez?

Chuck: Are you a guy, or a lady? Because I never heard the name Samus before so I don't know if it's a male or female name, and your voice filter sounds kinda unisex so I have no way to tell.
(Samus stares for a while)
Samus: Female. If that even matters.
Chuck: Thanks, sorry. Just wanna make sure I don't misgender anyone by accident.