I don't think there's anything shockingly bad in Season 2, and yes I'm including that favourite whipping boy of Voyager fans, Threshold, in that statement. I discovered, as with Season One, that I had much more patience with Season 2 overall this time around and found something to like in every episode more or less.
In approximate order:
Outstanding
Death Wish (One of the best episodes in all of Trek for me.)
Prototype (Not sure how this is regarded by most people but I've always found the menacing atmosphere that hangs over the entire episode particularly effective.)
Good
Resistance
Deadlock
Resolutions
The Thaw
Meld
The 37s
Elogium
Tuvix
Basics, Part 1
Dreadnought
Alliances
Lifesigns
Non Sequitur (Would have marked this down in the past but I found it weirdly enjoyable on last viewing. Against all the odds perhaps this has become my favourite Harry episode?)
Average
Twisted
Innocence
Cold Fire
Persistance of Vision
Parturition
Projections
Maneuvers
Threshold (I confess I never had the hate for this episode that most others seem to. Yes, I know it's stupid and contradicts established canon or whatever, and the science is appalling and Tom's makeup is bad and y'know the lizards... oh the lizards.... but.... I actually really like the rest of it; the stuff inbetween those other crappy parts.)
Below Average
Initiations (This is not *that* bad but I struggle to care about it, the Kazon are lame and 'Nog' is distracting.)
Tattoo (The Sky Spirits tosh is explanation enough.)