The first story starts off after the end of The Peacekeepers Wars with the intrepid Moya crew helping Dominar Rygel VXI regain his Hynerian throne.
Further comics series included all the Farscape universe canon putting the Moya crew into various adventures and tight spots.
You can find many details on the KRAD LiveJournal website. Including all the comic series cover art.
Here are the covers of the first three comic series in order of publication. Some of the comics overlapped on production dates. Plot descriptions are taken from the Farscape Comics website.

The crew helps Rygel regain his Hynerian throne.

After the events on Hyneria, the crew of Moya find themselves in the midst of a new, mysterious menace. But the crew will learn that their greatest enemies might just be themselves!

Zhaan and D’Argo are alive! Crichton’s not married to Aeryn anymore! What’s going on? Crichton tries to figure it out as he finds himself in an alternate timeline. While examining Aeryn and Crichton’s son, an accident occurred that sent Crichton off into this strange world.