There isn't any episode in S3 that I flat out don't like. Either the episode has something in it that is ultimately important for the Xindi arc, which saves it for me even though I tend not to re-watch it, or it has little to do with the overall arc, but I love the episode itself.
Hoshi and the Beast, er, Exile: adds a bit of information to the Xindi arc (location), and suggests in an oblique way how far they're willing to go for that information, but outside of the interesting camera work, it doesn't grab me.
Rajin: sets up Carpenter Street and the Degra-Human alliance, but there's no real explanation of why Archer thought he had to rescue this chick in the first place. And where the heck did she get all those skimpy changes of clothes?? They didn't have an extra set of coveralls?
Extinction: okay, the monkey language bothers me, and Hoshi's Carol-Kane-in-Taxi impression is like nails on chalkboard, so I watch it on mute. But I love the basic, heartbreaking story and I like to think that the Loqueque messed up Rajin's biological weapon vibe.
As to North Star and E2, even though they didn't add much if anything to the arc, they are just well-made episodes. North Star especially is a wonderful homage to the Saturday afternoon western and is magnificently shot. And with E2, I love that whole generational ship idea; like Twilight, it's "what could have been," but not so tragic. (E2 does have a faint echo in a later episode.)