I thought this a while ago with Basecamp. Although I'm sure they use it internally to manage their own projects, since they don't do client work anymore they're not using it for its primary use case, which is collaborating with clients.

It's not as huge a gap as with Haystack, to be sure, but anyone who's tried to get non-webhead clients to grok/use Basecamp will know what a struggle it can sometimes be. People have been asking for years for the app to have more help/guidance that's geared towards client end-users, rather than the agency account owner.

As for Haystack, I sort of see it as a (reverse) extension of their job boards, which seems to have been pretty successful for them despite not being something they themselves use very often.