His lawyers sent you a C&D; you responded to that C&D and now you've launched.
Considering he's been known as moot since 2003, and is known by millions of people as moot, and has a strong link to online discussion forums, I'd think he has an excellent case.
Since, apart from his name, the primary meaning of moot is "closed to debate" (not "open to debate"; you're welcome to provide examples of "moot point" where the meaning is "open to debate" and not "closed to debate") it seems like a weird choice of name.
But it's a weak case, because (as you imply) that original meaning has been obsolete for a long time, and in modern English people only use "moot" to mean "not worth debating". According to [4], "moot" began its pivot in the 16th century when law students used the word for practice debates where they would argue about mock issues—things that didn't really matter—in order to hone their skills.
Hmm, but then it is internet forum software, isn't it? "Arguing about things that don't matter" might be a perfect match!
1. http://en.wikipedia.org/wiki/Auto-antonym
2. http://dictionary.reference.com/browse/moot
3. http://www.merriam-webster.com/dictionary/moot
4. http://www.etymonline.com/index.php?allowed_in_frame=0&s...
If Moot were trademarked by 4chan (now there's a laughable proposition), there really would be a case - and a pretty strong one, at that. As it is, I imagine you're right that Moot has no real case against Moot.it, but it also sounds like the letter made no specific C&D demands.
I imagine your product can rise above this based on its merit, but you gotta acknowledge the subtle trolling inherent in the name. I understand why you can't publicly acknowledge this, but it's there anyway.
Speaking strictly about the branding I really think it doesn't matter whether the inherent meaning is closed or open. Product naming is an art form and it doesn't have to be realistic.
I hope we can use Moot successfully on our issue tracker
So we can "close the debate" on those moots :)
"Yeah, anarchy! Wait, I can't have everything my way?"
http://www.bbc.co.uk/news/technology-20408037