The novel series that I am trying to identify was being published around the same time as Goosebumps and Animorphs though was not as popular and the subject matter what rather dark at times. Each novel was usually unrelated to each other and though I can't recall any titles I'll try to describe details I remember from some of the books I read way back in the day. The covers of these novels were very unique and somewhat minimalist and appeared to be computer generated graphics (like a video game screenshot) rather than paintings or illustrations.
One of the novels is about aliens abducting a brother and sister from an airplane in order to get an evil type of alien out of the sister's body. A particular detail I remember was the sister reliving a repressed memory about the evil alien (which was like a black liquid cloud) hurting her.
Another novel is about a teenage girl and friend and a mysterious lake monster. A particular detail I remember was the monster swims next to the girl in the night and she touches it with her fingers and the scales cut her skin.
Another novel actually takes one of the characters from the lake monster book and tells another story about dinosaurs still alive and loose on an island. I think that this novel was the first one where the cover designs departed from the computer graphics and took on the more banal cartoony illustrations.
Finally, a mini-series in the collection of novels that were all related were about a boy who discovers a gremlin-like creature called a Buru. This mini-series is more supernatural featuring various crypotozoological creatures, shape-shifting children and a dangerous game where teams of people and creatures from other realms compete to collect objects or artifacts and the creature called "The Collector" is the top player in this game.
I've racked my memory for more concrete information, but this is the best I can do and I hope the information is sufficient enough to jog someone's memory.