I don't know about a complete shared Hanna-Barbera Cinematic Universe (HBCU), but I've long thought that H-B's adventure, sci-fi, and fantasy shows would work great in a shared movie universe (largely because H-B did it themselves originally).
Space Ghost, Jonny Quest, Birdman, Galaxy Trio, Herculoids, Mightor, Samson & Goliath, and Teen Force should work well together. With some tweaked/expanded world building Galtar and the Golden Lance and Pirates of Dark Water should fit in nicely too. Depending on the where the rights lie (and perhaps with some reworking) Sky Commanders should fit well. And since the Ruby-Spears library is effectively coupled to the HB library we might be able to bring Thundarr the Barbarian and The Centurions into the fold.
Things don't necessarily mesh as well once you start bringing Clue Club and Jabberjaw or Huckleberry Hound and Quickdraw McGraw to the above. I suppose it could work, though a completely shared HBCU would be a mighty strange place.
Who knows what evil lurks in the hearts of men?