These are children’s mystery story series that have spooky themes. Not all of the individual books in each of the series are spooky, but most are. Most of them fall under the category of Pseudo-Ghost Stories, which are stories that I frequently think of as being like Scooby-Doo, where there are mysteries that seem to be about ghosts or other supernatural events but which turn out to have other, more conventional explanations.
About a girl in elementary school who solves mysteries with the help of her friends, who call themselves The Martians. Not all of the books in the series are spooky mysteries, but a few are. By Susan Pearson.
Mary Rose and Jo-Beth Mysteries
About a pair of sisters who live in Indiana and have adventures on road trips with their father. Not all of the books in the series are spooky mysteries, but a couple are. Written by Eth Clifford.
J. Huntley English is a boy genius who also happens to believe in monsters and wants to find real ones. With his friends, he investigates strange phenomena and odd people in their small town in Pennsylvania. By Drew Stevenson.
The adopted son of a famous judge helps him to solve mysteries in feudal Japan. Not a series for young children! By Dorothy and Thomas Hoobler.
About a girl who wants to be a detective and her two friends. They investigate spooky mysteries in a small town in Pennsylvania. By Drew Stevenson.
Sherlock Holmes’ Tales of Terror
Sherlock Holmes and his friend Dr. Watson solve spooky mysteries with supernatural themes and Christian morals. By Kel Richards. 1997.
The Stanleys are a blended family, and the children solve mysteries, sometimes with a spooky theme. By Zilpha Keatley Snyder.
A group of third graders investigates strange phenomena and possible ghosts, including one at their school. By Grace Maccarone.
The Three Investigators Series
Three friends form a detective business, using a trailer in a salvage yard as their headquarters.
Jestress's Forgotten Books and Stories 