What I've found to help, when doing a niche comic (or obscure comic reference) is to find a way to subtly explain the back story of the niche or reference without taking too long. Not an easy task. Serial comics work well for this, but again, if the reader isn't familiar with the material, then they may not find it funny.
Usually my obscure comics involve fight club or tv bits that I've watched. When I do these I try to explain through humor (or character dialog) what the back story is. If I can't do this easily, I will at the very least try to broaden the comedy/punchline to something most people can relate to.
So to make a long story short (too late) it's not easy, but it's doable. Keep tryin', man.