Oh, where do I start with this one? When I decided to make Bob's alternate gay, I knew it could be a rather touchy subject with some readers. It's one thing to use someone's stupidity as the butt of a joke, but a person's sexual orientation is off-limits for some people. So while there might be some jokes concerning Alternate Bob homosexuality, that itself is not the joke; the joke is how other characters react to his homosexuality. For example, in this comic, Alternate Bob isn't acting in a stereotypically homosexual manner because he's gay, he's acting that way because he's messing with Bob, because he knows exactly how Bob will respond to that kind of personality. Notice how his expression changes as the comic progresses?
That being said, I'm not saying Alternate Bob doesn't actually like his purple scarf or Bob's black scarf, but he's not really suggesting that he would "be all over" Bob, because, well, that would just be weird. By the way, I have absolutely no idea what "Merv's" is. I'm guessing it's some sort of clothing store, but I really don't know.
Oh, and that limp-wristed hand sprite is actually part of the Proto Man sprite sheet. It's from the animation in Megaman 7 where Proto Man throws his shield to Mega Man after being defeated in combat. Seriously.