I know how everyone feels when they've written this glorious and wonderful post and have it fall into the ether. That's the case with my discussion of Star Trek comics.
Anyhow, where to begin? My all-time favorite Classic Trek story came out in hardcover and was written by Chris Clarement and Adam Kubert. Great story and great art.
Also, IDW is producing many good titles these days. I do wish they'd get the rights to Deep Space Nine and Voyager at least.
My favorite miniseries iis "Klingon: Blood Will Tell." This was advertised as "the view from the other side," and I figured it would just be a mirror of the Klingons in there. Nope, it seamlessly got all the Trek appearances together then had a battle royal in the shadow of Star Trek VI.
If you like aliens, check out the Alien Spotlight. One was a John Byrne story on Romulans via Caligula. It did so well that they're doing another set, with the first issue on the Tribbles and a second one on the Klingons (which is as close as the turtleheads would like it).
If you like Dorothy Fontana, she wrote "Star Trek: Year 1, Part 2." or something like that. If you wonder whatever happened to Arex and the female Romulan commander, you'll find out here with pencilling by (IMHO) the best artist in the Trekiverse, Gordon Purcell.
For some reason, the TNG series hasn't thrilled me. I still don't know what happened at the end of their first series, and then the TNG Enterptise D goes searching for intelligence, and doesn't find any!
But the latest Next Gen series does a "what if" story on what would have happened if Kirk had been killed before the big battle in Star Trek VI, which mostly puts NOP (Not Our Picard) on the front line of rebels agains the Klingons who have captured Earth. The final page of this series is worth the price of administration. Oh, and Wesley gets a craaaaaaaaaaaaazy hairstyle.
Peter David brings his New Frontier to IDW with a series featuring the characters from his series of novels. John Byrne wrote new adventures for Gary Seven and his perky companion in what is not surprisingly called "Assignment Earth.'
I'll wrap this up. John Byrne delivers a miniseries explaining the battles and prejudice enountered by "Number One" under Christopher Pike. There's also a great story that ties the first Enterprise mission with the crew's last clash, including why Kirk, Spock and McCoy went their separate ways before ST:TMP.
There's also a cool Alien Spotlight series that focuses on Tribbles and then Klingon (though not in the same issue).
Sorry if I ran two long. I was a comic reader for a decade before I beamed into the Enterprise. I hope you find some good stuff in there. IDW is also publishing compiled trade paperbacks.
I concentrated on the modern stuff because it gets mighty quiet when there weren't Trek comics around, and that wasn't long ago.