Tough question. I'm going to go with my favorite but also give honorable mentions to a couple of others. Choosing only one it would have to be Lt. Velorek from The Way We Weren't. He was played by Alex Dimitriades who I'd never seen before in anything but after this episode I Googled to find out more about him. Talk about a scene stealer! I didn't think anybody could steal a scene from Claudia Black but he came close. In the story he is seen only in flashbacks from three cycles prior. He is in charge of Capt. Crais's experiment to breed a Leviathan gunship. Fairly quickly we see that he has feelings that seem to run deeper than typical Peacekeepers. We uncover that these feelings include Aeryn whom he arranged to be transferred to his unit. The revelation of their relationship and her eventual betrayal of Velorek are among the most gut wrenching in the Farscape universe up to that point. Velorek needs to convey a great deal of information about Pilot, about Leviathans, about Crais and the experiment, about the possibility of Peacekeepers being "more". The actor does this by using his eyes and gestures (recall the touching of Pilot's face) to great effect, providing the layering that the script would not have time to cover.
The knowledge of Aeryn's prior relationship also leads to the start, in my view, of the deeper emotional connection between John and Aeryn. Specifically the ending of the episode when John asks Aeryn if she "loved this man." The subtext of her ability to love, the juxtaposition of her revealing that the first time she met John he spoke the same words as her former lover once did, "You can be more", all lead the audience to see for the first time that there are deeper feelings underpinning the more obvious chemistry.
This answer would not be complete, however, without two honorable mentions. First, Gunslip, I mean, Gruntlick, no? Okay, I'm talking about Hugh Keays-Byrne portrayal of Grunchlk in the season two ender Die Me Dichotomy. He was especially outstanding when he was portraying himself being controlled by Scorpius. This twice removed characterization was wonderfully creepy to watch.
The second honorable mention is for Kent McCord who played Jack Chrichton as well as Ancient Jack. He is my favorite guest character spanning the entire series. Faced with the most outrageous situations, such as those in Won't Get Fooled Again, he played it dead straight. This gave the humor an edge that I believe ultimately came to define Farscape.