I mean the names that you're surprised about their lack of use, rather than names like Keren-Happuch which you can quite easily understand why they're not used much 
For example, I adore Moses. I think it's perfect. But I've never met a person called Moses in all my life. I also think it's odd how Noah is so popular but Shem, the name of one of his sons, isn't popular. To me, Shem is a nice name and seems usable.
I also always expect Phineas to become popular considering the popularity of Finn/Finley/Finnian... Just Finn names in general which are everywhere lately.
For girls, I always think Mahlah and Noa are pretty names and they also seem like pretty cool, strong biblical namesakes too. Yet I have never heard of a Mahlah being used (maybe because a Google search declares the meaning of the name to be 'sickness' which is incorrect?) and while Noa is known and often suggested on baby name boards, it always seems to be shot down by other posters and not chosen.
Lastly my beloved Zephaniah. I think this name is soft and gorgeous and I also think Zeph is a lovely nickname. But I never hear it. Maybe it's just too long.
There's so many other bible names that I adore like Josiah, Isaiah, Silas, Esther, Martha etc but they all seem much more well-used. I want to hear the names that you feel aren't as well-used as they deserve to be!