The Real Question
I think the answer doesn't depend on the stigma that might come with it for applying for a job, but on whether or not you'd want to work for a company that would stigmatize it.
I mean, this is something you developed and that:
- definitely shows off your skills,
- and possibly outlines some of your political, morale, ethical stances.
Obviously, this is going to be interpreted by the person reading your resume. But you should ask yourself if it's a worry to you that they will care and it might impact your daily job (as opposed as worrying about getting the job itself).
That being said, if you have enough experience and show-off projects on your resume and these grey-area items don't relate at all to your target job's domain, then you might as well leave them off to avoid friction.
Or, you can be careful to not give details on the job's domain, but only outline technical challenges. Though that could invite follow-up questions, of course.
Wait, That Wasn't the "Real" Question Yet...
Whether you care about the stigma is one thing and implies you'd have already decided on the (il)legitimacy of your projects.
Therefore, on a higher-level, you obviously want to ask yourself if you should have worked (and should work in the future) on these grey areas projects. As an extension of a well-knowngeneral ethics rule, this would be: if you'd be uncomfortable with kids (and people in general) watching over your shoulder while coding these, then you probably shouldn't. (Of course that's not to take literally: there are plenty of legit and ethical actions that could be uncomfortable to undertake in certain scenarios: fear of repression in a totalitarian state, for instance)
That's mostly up to you to answer and that's why these are of grey. But if it's going to be more of a problem for you in the general case and it's not the kind that falls in the category of vigilant-superhero-night-life, I'd suppose it means you're better off.
I don't think bittorrent wouldn't really carry any sort of stigma. The protocol/technology itself is legit and a modern times solution to a modern times problem. That it first found (and still finds) applications in tendencious fields is anecdotal at best.
I would probably put anything on my resume that doesn't directly show "intent" to commit something illegal. Working on ThePirateBay doesn't necessarily (but that's subjective). Working on a trojan horse would (if presented as such, and not as a RAT). Yet again that'd depend on the target employer's field, but that'd be my rule of thumb.
Conversation with a Stranger
Writing the above I think I'll summarize it best like this: I'd use the same rule of thumb as for a conversation with a stranger. I'd be comfortable putting on my resume any project or experience that I'd be comfortable to address or mention in a conversation with a stranger tackling a tendencious discussion topic and where I'd be defending my position, even if opinionated and borderline. Things I wouldn't be comfortable to discuss are probably things I'd probably leave off a resume.