Looking over Fast Learner's list, I'm reminded of why I don't buy the argument of "The Academy doesn't like fantasy movies" as the reason why RotK won't win best picture.
If a genre movie from a genre currently in disfavor with the Academy members or looked down upon by the Academy members can transcend the boundaries of that genre, or can elevate that genre to new heights, or can reinvent that genre, the Academy will embrace it.
"The Academy doesn't like slasher/horror movies." Well, they liked "Silence of the Lambs."
"The Academy doesn't like Westerns anymore. They're dead." Well, they liked "Unforgiven."
"The Academy doesn't like musicals anymore. They're too old-fashioned, too unbelievable for hip, modern audiences." Well, they liked "Chicago."
The LotR films have certainly reinvented the genre (for the big screen, anyway), and have have elevated it to new heights. For some, it even transcends the boundaries. I don't think it being a fantasy will be that big of a hindrance with the Academy. They may dislike it for other reasons (jealousy, jingoism, spite, Jackson departed from the book), but I don't think it will be because it was a fantasy.