Well, there's the Phantom Stranger. His origin story is full of mystery. He seems to be an otherworldly being, but the exact details of how he came to be are very much in the shadows. There are also hints of some kind of cosmic or divine purpose to his existence, which makes it all the more obscure. Then there's Mister Miracle. His origin ties in with the Fourth World of Jack Kirby's creation. It's not as well - known as Superman's origin, for instance. He comes from a world of gods and war and has to escape to Earth, but the whole concept of the Fourth World and his place in it is quite complex and obscure.
Take Hellboy for example. His origin is that he was summoned from Hell by Nazi occultists during World War II, but then he was raised by the good guys. This origin is not your typical superhero origin. It has elements of the supernatural, dark magic, and historical events all mashed together in a rather unique and somewhat obscure way. Another one is Swamp Thing. He was created when a scientist was killed in a swamp and his body merged with the plant life there. This origin is not as common as others and has a very different and somewhat hidden backstory that makes it an obscure superhero origin.