For the most part, "Eureka" continues to be funny and absurd. But this season I felt there were a couple of off notes ...
In their pursuit of a long-running adversary, the show-runners have created an "artifact" (which is itself a problem - both for the characters and the structure of the show) and a shadowy conspiracy that wants access to the artifact. Last season ended with a death related to the artifact - and that's driven Henry's (Joe Morton) behaviour all season.
In pursuit of comedy, we have Carter (Colin Ferguson) claiming he goes to the gym all the time. We're supposed to believe that he doesn't, as they use his ineptness in the gym as "comedy." But there are several problems with this. We've seen Carter without a shirt before, and it's clear he goes to the gym regularly. Another problem is that he's lying to try to make himself look good. While they occasionally show him trying to pretend he understands advanced scientific concepts to avoid looking foolish, lying hasn't generally been his style. Finally, the scene wasn't actually funny. If you can't make a scene funny without warping a character's behaviour to suit the comedy, you're really doing something wrong.
In the final couple episodes, several of the main characters all betray each other (all with the best of intentions), except for Carter who is of course standing in the middle trying to figure it out. It struck me as sloppy and more than usually absurd.