This is harder than you'd think at first. There must be dozens of princesses on SNES: the problem is that about half of them are essentially the same person.

I think I'd go:

Total cop-out answer: Melody (Princess Maker; Legend of Another World) - While not named directly in the game, she's named in other products of the same company. Since the game is about how she develops as a person, she can become almost anyone in the game's dozens of endings. She could fit Fuck, Marry, or Kill. However, she's the player character's daughter, which makes all three options feel really weird, and she's only a princess in a few of the endings.

Fuck: Sarisa (Final Fantasy V) - Most of the SNES princesses seem too delicate to be able to handle casual sex. I think with Sarisa's rough childhood, growing up with unsavory characters, she'd be best able to handle it.

Marry: Elle (Terranigma) - Elle is definitely one of the deepest princesses on the SNES. (Karen of Illusion of Gaia is as well, but she's too young and she's a brat.) Elle is a character you get to know and grow attached to, and she's a genuinely good person, even if you don't always get along with her.

Kill: Mileena (Mortal Kombat 2) - This might be a bit of a cop-out. Mileena is a clone of Princess Kitana, so I figure that makes her kinda a princess too. She's definitely the most evil and brutal princess I can think of on the SNES, and the one I'd feel the least guilt over killing. Though to be honest, she'd probably kill me if I tried.