The Adventures of Teddy Ruxpin had surprisingly good animation and writing.
In the early 80s there was a weird cartoon called Pandamonium, about three pandas who could merge together to make some kind of superpanda. They traveled the world with a couple of humans trying to protect it from an evil alien called Montragor. It was an early production of Marvel Animation and little of it survives online now.
Saturday Supercade adapted arcade games (and also Pitfall) into short cartoon episodes. It featured the first cartoon version of Mario and Donkey Kong, long before any others. Pitfall's supporting characters Rhonda and Quickclaw made appearances in the Pitfall II: Lost Caverns game.
The Real Ghostbusters wasn't really obscure, but J. Michael Straczynski wrote for it, and he wrote an episode involving Cthulhu. (He also was story editor on He-Man, and penned the episode it was revealed that Teela was The Sorceress's daughter.)
There are a number of cartoons that Cartoon Network hyped up then just kind of forgot about: Mike, Lu and Og, Sheep in the Big City and Whatever Happened to Robot Jones are three in particular.
