To paraphrase an old joke, and risk the disapproval of Dave Clarke and Daniel E. Shub: What do you call someone whose PhD thesis contains a frivolous epigraph that they spent a while finding? Answer: "Doctor"!
Keep in mind that to first order, nobody will ever read your thesis. Ok, you will, and your advisor will probably read most of it, and perhaps some of her future students will look through it for ideas. And your family might flip through the first few pages to be polite. Otherwise, what people will read are the papers you publish based on it. Therefore, it doesn't really matter very much whether you include an epigraph or not, as few will read the thesis, and fewer will notice the epigraph.
Personally, I enjoyed choosing a "frivolous" epigraph for my thesis; it did take an hour or two that I could have spent writing, but nobody can spend all their time writing, and it was a good stress reliever. I don't think it enhances the thesis, particularly; I don't really think it affects its merit at all. But it was one more little thing that helped me get through the process.
Certainly, your epigraph should be in good taste, and not offensive to anyone. Don't use it as a way to make the thesis sound more impressive; that's a waste of time, because nobody will be impressed. And if your advisor notices it and objects for any reason, apologize and meekly remove it. But otherwise, if you have fun with it, I can see no reason to object.