Off the top of my head...
Vulcan's Forge and Spock's hometown of Shi'Kar are from "Yesteryear"
The USS Antaries seen in TOS-R: "Charlie X" is based on the cargo drone ships from "More Tribbles, More Troubles"
Kor's old ship, the Klothos, was seen in "The Time Trap" (although Kor called it a D-5, when in TAS we see that it's a D-7. But he was going senile, so...)
The first holodeck is seen (called a "rec room") in "The Practical Joker.
Kirk's middle name "Tiberius" is from "Bem"
Also Captain Robert April was first seen in "The Counter-Clock Incident"