I still have all my star trek comics, which is why i didnt buy the CD. I have the entire first marvel run, first DC run(TOS/TNG), second DC run(TOS/TNG), entire second marvel run, all of the wildstorm stuff, up to the IDW stuff. Granted, some of the older issues from back in the day or no longer in the best condition, but i still read them all the time. I know just about every panel by heart.
Here's my personal top ten story list, including material from all the above:
10.Retrospect(DC I, TOS Annual#3)Incredible Scotty story
9. The Way of the Warrior(DC II, TNG#33-36) Great story where Q turns the crew into klingons to prove how terrible they are as a species.
8. Klingons: Blood Will Tell(IDW) best story yet from IDW in my opinion
7. Timecrime(DC II, TOS#53-57)Great time travel story where the Klingons and the federation are allies in Kirk's time. The timeline has to be fixed
6. The Worst of Both Worlds(DC II, TNG#47-50). The Enterprise falls into a parallel universe where the Borg won.
5. The Modala Imperative(DC II, 8 issue mini) A cross-over story involving both TOS and TNG.
4. The Trial of James T. Kirk(DC II, TOS#10-12) This story was built up from the preceding 9 issues, involving the repurcussions of Kirk's actions involving the klingons in star trek III.
3. Star Trek: Early Voyages(Marvel II, entire series) I can't pick a favorite story with this series, the whole thing was so good.
2. War and Madness(DC II, TNG#71-75)
Great story involving the tholians, the borg and the klingons, set shortly after "All Good Things,,,"
1. The Mirror Universe Saga(DC I, TOS#9-16)
IMO, the best star trek comic ever written