Les Misérables: Shōjo Cosette is a very underrated Аниме in my opinion.Even though it is for children and therefore has a few changes,it still remains the most faithful adaption of Victor Hugo's classic novel and it is 100 times better than the overrated but beloved musical.
I was torn, but I'm going to have to go with Detective Academy Q. For what it is, it's seriously underrated. The fanbase is nearly non-existent and it really is enjoyable, at least until the plot change near the end. I never actually finished it, though I heard neither did the creators. After watching 90+ episodes of Case Closed/Detective Conan, I can't say which is "better" but they deserve equal popularity at least.