[quote:1kqhp4ar]However, you could apply the arguments you just made to, say, fanfiction, fan art, or sprite comics. I don't see anyone giving THEM cease and desist orders.[/quote:1kqhp4ar]
Fan fiction and fan art are works created by individuals. A sprite rip is not... it's straight up theft of someone else's work. And even so, fan fiction is still technically an infringement on intellectual property rights. You couldn't, say, sell your own novel featuring Buffy the Vampire Slayer and Bilbo Baggins as your main characters, because someone else owns the rights to those characters.
And I wouldn't say most companies approve of fanfiction or fangames... more like they tolerate them. Sure, there are always exceptions, such as with Black Mesa, but for the most part the official stance is always "do not use without permission." The reason so many fangames and fanfic sites can run rampant is because for the most part they are completely harmless. A company generally isn't going to interfere with your fan creations unless it threatens their profit margin somehow, because it's just not worth the time, effort, or money.
But just because they probably won't doesn't mean they can't... they're well within their rights to stop you if they see fit.
[quote:1kqhp4ar]when there's an entire online expo devoted to fan-games, it's obvious that anyone who does have a problem with it is in the minority.[/quote:1kqhp4ar]
I would say that's debatable. While a large number game developers don't see anything wrong with fangames or sprite ripping, there are just as many who do. Personally I'm not terribly big on fangames, but I'm not all that hardcore about the issue. I say do whatever you like. Though I do think that original work is always a better option.