Yep. Organians too,Trelaine's and Charlie X's people, and so on. Even the "Friendly Angel" from "Miri" and Apollo from "Who Mourns for Adonais?" are probably still bouncing around out there and did their fair share of fiddling around with their pet human playthings.
Who's species does the Sha-Ka-Ree "God Thing" from TFF belong to, who were powerful enough to banish it at the center of the galaxy behind an energy barrier? For that matter, who built the outer barrier that had the power to turn Gary Mitchell himself into a god-like being? Who built the various planets that look exactly like Earth? Which one is the orignial? Ours or someone else's? And for what purpose?
Moving into the 24th century, we see Q, DS9's Wormhole Aliens and TNG's Douwd ("The Survivors").
Who built the Doomsday planet killer from TOS? Was it Guinan's people to fight the Borg, as seen in "Vendetta" or someone else? What are the Al Aureans anyway that Q would actually be afraid of Guinan upon first meeting?
The galaxy is full of "Old Ones" who like to meddle in our collective affairs. We can definitely add the Red Angel to that list, who may be related to one of those super-being species.