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.
I just started reading the series recently, I'm somewhere in the 20s a the moment. I found the Klingon War story line and the mirror universe stuff particularly impressive, and agree how well they integrate into the films is really well done. I've found the stand-alone issues less engaging, but overall I'm impressed, this sort of strong building of a distinct continuity and development of secondary characters is something I associate with the modern age of trek-lit and am pleasantly surprised to find in older material.
Well in the time before TNG, Trek lit had a bit more freedom. It was really with the TNG era that-- I felt-- that Trek Lit took a step back.
Now I will admit that DC Comics run had some clunkers: Sulu in a giant Mech Fight; Kirk and Co. keeping the BoP stored inside Excelsior (which was turned into a massive starship); things like that. But on average, the series was some of the best "Trek out there.