Whoa. Loaded question!
Well, there was that race that saved Charlie X, but made him not human in the process. I don't think we ever got their names.
There was a race called the Meltrons, I think, that pitted Capt. Kirk in individual battle against that huge reptile ship captain (I think the reptiles were called the Gorn).
Then there were the Organians, who stopped a war between the Klingons and the Federation.
General Trelane's species seemed advanced enough to be first ones.
Then there was that ancient race that shed their bodies and put their essences into spheres -- only three were left by the time the Enteprise found them, but they were still quite advanced.
Then there was that group of brains that bet on the gladitor games, the race from the pilot episode on Talos IV; and the race that tortured McCoy so an alien female (Jem?) could learn compassion, which would in turn earn her race the right to be saved from a super nova.
Come to think of it, the TOS crew met quite a few super species.
In TNG, besides the Q, there was an entity in season II that put the Enteprise in a maze and did experiments.
There was also that fellow who wiped out an entire race just by thinking about it, because that culture attacked the colony where he and he human wife were living...
In DS9, we see the wormhole aliens -- both the Prophets and the Pagh Wraiths -- I think they'd qualify...
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"What's up, Drakh?"
Michael Garibaldi