Father/daughter then mother/son. Brother/sister in distant third, and all others lose that spark of the illicit incest imparts.
The difference between F/D and M/S, to me, is degree of taboo. I see the former as eking out a win in that contest, purely because of what each relationship is meant to be.
A mother should, generally, be the nurturer to her family, and especially her children. She's motivated to care for them and ensure they're emotionally healthy while having all their needs met. It's a short hop from nurturing to coddling, and incest is the ultimate form of coddling. A mother is giving up her dignity and propriety for the sake of "helping" her son with his sexual urges. It's wrong, yes, but it's still sort of in line with her stated aim of caring for him, except now she's taken it too far.
A father, on the other hand, is the protector and material provider of his family. He is meant to drive off bad romantic prospects and ensure nobody takes advantage of his little girl. Him substituting himself in for any potential suitor is less a perversion and more a total inversion of both drives. He is handing her the worst suitor he can (she can't even discuss their relationship with others, due to social disgust if not outright criminal conviction) and taking advantage of her in the most absolute way he can manage. He's doing the worst possible thing he could for her, knowingly, and yet it's all for love. It's horribly messed up, and that's the basis for incest. The entire fetish is, when you really think about it, tragic and disturbing yet wholesome and loving, all at once. Father/daughter stuff is the perfect marriage of both extremes.
Then there's the imbalance of the relationships. Guys tend to more often be dominant, and women more often submissive. A mother holds power over her son, yet by sexually submitting to him (as is often the case in these types of stories), she bridges the gap and makes their positions more equal. She is older, yet he's the one in control. She's in charge in public, but he's in charge in the bedroom. They trade dominance as required, assuming he doesn't just take over her whole life.
A father dominating his daughter only widens the gulf of power. She's both younger than him, thus beholden to his commands, and now sexually submissive to him. He dominates her in every possible way in all aspects of life. She has, essentially, come under full submission to him, which will only end if she decides to go off and find someone else to romance. More often than not, his control over her is such that he can nip that idea in the bud, so she's unlikely to ever leave.
Then there's the relative rarity of F/D incest content compared to M/S fare. It might not be the case in the Games+ section of this site, but usually there's a glut of sons and brothers seducing mothers and sisters, with the corollary being relatively rare. I don't know why that is, but it's the pattern. It holds true for other media as well; erotic stories, comics, manga, all of it more often goes with a son taking his mother or a brother seducing his sister than a dad dominating his daughter. The rarity adds to the taboo somewhat, since it seems as if father/daughter content is too illicit even for this genre of porn.
Then, of course, there's the fact that large things entering small holes is just really gratifying, and a large dick always looks most at home on an adult frame.