Those Series 1 comics were some of the best 'Trek stories ever.
-- The issue, post ST IV, where Kirk has to face up to the fact that his "legend" might be a bad example to younger cadets. I think the title was "Repercussions" (probably got it wrong), where a young ensign is thrown into command of a training ship when the senior officers are killed in a Romulan attack and the kid spends the whole issue trying to do what Kirk would do, only to get his ass handed to him.
-- Spock's tenure as captain of the USS Surak
-- The "Death" of Captain Kirk, and the "ghost" of Christopher Pike warning him to give up command before it destroys him.
Yeah that issue was called "Idol Threats." My two favorite story arcs were the Mirror Universe(#9-16) and Who Killed Captain Kirk(#48-55). What I liked most about the first series is how well they were able to integrate their stories between Star Trek II, III and IV.