Earliest memory has to be from Devil in the Dark, mostly because of the aliens POV hunting down & melting the redshits into acidic smoking slag! Followed by Kirk & Spock exploring the tunnels & caves. The alien was the weirdest design I'd seen on screen + I thought its magma crust would burn Spock or at least have his eyebrows singed off! but it kinda looks like pizza now 
Second one are vague memorys of the parasites from Operation Annihilate, mostly due to the buzzing sound design & their stingers, the deflating sound effects are a bit funny & the flying by strings took a bit of the scare factor away though. Its good that Trek helped to introduce the idea that alien life isnt all warm & fuzzy and could be a nasty parasite! A scary theme brought up later in the Alien movies.
McCoy screaming like a madman on cordrazine - Murderers! Assassins!
Lastly the Balok puppet head, scary & still very freaky looking still to this day.

Second one are vague memorys of the parasites from Operation Annihilate, mostly due to the buzzing sound design & their stingers, the deflating sound effects are a bit funny & the flying by strings took a bit of the scare factor away though. Its good that Trek helped to introduce the idea that alien life isnt all warm & fuzzy and could be a nasty parasite! A scary theme brought up later in the Alien movies.
McCoy screaming like a madman on cordrazine - Murderers! Assassins!
Lastly the Balok puppet head, scary & still very freaky looking still to this day.