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.