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.