I will keep only animes I actually like, but I did also consumed a lot of obscure trash in my lifetime.
Fushigiboshi no Futagohime
Just a cute magical girl show about twin princesses. Even though this one is a Junichi Satou show, not even his fans seens to want to watch this lol
Mahou no Stage Fancy Lala
Weirdly enough, it is a bit more known than some really good Toei magical girls, but you still have to dig quite a bit inside the magical girl niche to hear about most Pierrot magical girls aside of Creamy Mami.
Actually very fun show about a girl living with 6 clones of her. Just like the name implies, I'm convinced there are exactly 7 fans of this show scattered across earth.
Cosmic Baton Girl Comet-san
One of the best magical girl shows I've watched, but also one that only got a complete fan translation very recently. Despite having style, music and a mood that could easily rival something like Doremi, no one even knows this thing exist.
Fushigi Mahou Fun Fun Pharmacy
Probably the least known good Toei Magical Girl, despite most episodes being 12 minutes long, it has a pretty interesting universe and a lovable protagonist. That show also oozes style in a way you would expect from those weird Toei shows.
The entire Jewelpet franchise is unknown outside of japan, but Happiness is so good, I find it a crime even people who are interested in this series stops watching before even give this season a chance. Like any other Jewelpet, you don't need any knowledge about the other series to watch. It's just a very solid cute girls doing cute things show with some surreal comedy.
A very stylish show about a gothic lolita learning science with a bunch of caricatures of historical figures. Do I really gotta explain why most people won't watch an educational show about science?
Kamisama Minarai: Himitsu no Cocotama
As you would probably guess, the niche of shows about cute animals is not very popular, and what happens when you are unknown inside the unknown niche? Exactly! No one watches you! I'm yet to talk to another person who actually watched it. But's a pretty fun anime.
Most of those shows have under 500 completed watches on Anilist. My take away from most of this is that people just don't like watching shows made for girls. Which is understandable.
I never watched the anime but the PS2 games were pretty kickass.
I don't really hang out with otaku so I don't know if these are genuinely unknown but I reckon the earliest anime series I watched on tv would be considered obscure by now on account of being relatively old (just like me I guess) and not part of any famous franchise (definitely like me).
Same goes for a number of lesser known shows, some of which like Silent Möbius only aired once, often late at night, so you better not forget to program your vcr.
E.g:
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Robin Hood, Saber Rider and Treasure Island
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Phantom Quest Corporation, Silent Möbius and Golden Boy
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Arjuna (aka Earthgirl Arjuna), Noir and the Candidate for Goddess which I probably liked only because it reminded me a little of Zone of the Enders.
Takarajima is so good, I'm glad I watched it. But yeah, pretty much everyone I knows that watched this show were Osamu Dezaki fans.
but it's pretty light-hearted and silly. 
