I have listened to the old Podtoids Jim was a part of where he talked about all of this on "Shadow Complex", and if it bothers you, you can always counteract everything they say by doing something else.
Phil Fish says Japanese Games suck, so buy Fez, probably because it is a good game (As long as Fish doesn't say he hates PS3 so that I might get to play Fez, that'd be wonderful, because it looks like of awesome) and then buy something from Atlus or whatever particularly Japanese, which says "Hey, I appreciate your game, not necessarily you, but I'm buying a game from the Japanese that I know/heard is good."
Now, I have heard about the Doug TenNapel thing, but I truly took that as a trolling thing, and less of a homosexual slam. However, if that is true (Let's take it as real for the sake of this conversation), I love Earthworm Jim. I own it on PSN, I own both 1 and 2 on SNES, and I own EWJ 3D for the N64. To suddenly take everything I love and invalidate it as "He hates something, now it sucks" is incredibly childish.
If he made an Earthworm Jim game with Shiny at the helm, I would play it. If a movie came out with EWJ (or by Proxy, TenNapel's name on it), I'd see it. I have seen Sockbaby [http://sockbaby.com/] more times then I care to imagine, and it's brilliant all the way around. I'm not going to avoid a 5th episode should it ever come because of something the Creator said. He just doesn't like Gay people, and that's his prerogative, I can counteract his ways by giving money to a gay rights group, then they make money and I get to have a good time with a game or movie.