I have to say, I especially liked the Augments arc. I can't really articulate as to why, but I'll try anyway.
Brent Spiner was awesome as Erik Soong, and while I found his turn-around at the end cliched, his character was still interesting, and I also liked the Augments themselves. I kind of wished the one without any super-human strength had been developed more, though. I also wished that some of the Augments had been allowed to surrender rather than their insane leader killing them all, and I really thought his cliched undetected beam-over robbed his "death" of what it could have been. Other than that I thought those three episodes were pretty good.
I also liked the Klingon arc, despite the fact I never really cared for the Klingons being on the show. As with the Vulcans, the Klingons had kind of been screwed up a bit, and while some people apparently wanted to go on pretending the Klingons always looked as they pretty much always have from ST3 onwards, like it or not
Trials and Tribble-ations acknowledged the difference, and went out of its way to recreate TOS, much to the butt-hurt of reboot advocated and JJ fans everywhere. However, unlike the way the Vulcans were "fixed", the way the Klingons' appearance was established as changing was actually pretty decent, and in my mind at least somewhat believable. I only really have a couple of nitpicks, one being Reed's sudden ret-conned association with an organization that IMO shouldn't have existed yet, and the other being the unintentionally hilarious way Archer just charged to the rescue all on his own.
The only other strong episode of the season, I felt, was
Observer Effect. While the idea of having aliens take over crewmembers was nothing new and is usually boring or stupid, I thought they did a pretty good job in this episode with that. While I could have done without ti-kwan-Hoshi, I liked the way they brought back something of that brother/sister friendship between Hoshi and Trip, which really hadn't been played with for over a season. I also liked the way Archer was presented in this episode, as a leader I could respect, and someone who deserved the loyalty we have basically just been told his crew had for him. For once, it's actually completely believable that Archer would be the one to try to selflessly rescue his crewmembers, since one of them was supposed to be his best friend, and the other was basically the greenhorn - basically stuff that had been lost for a long time coming back, good things too. I also found the scene where he put his hand on Trip's chest as he died to be very poignant, and I can honestly say it touched me on a deep level.
IaMD I liked, but it wasn't so much for it being "strong" so much as just fun.