Mine has to be how sickly out of control Warriors were in Vanilla, how disgustingly overpowered Restoration Druids and Warlocks were in TBC and not to mention Death Knights and Ret paladins in WotLK... *shudders*
For Cataclysm it's pretty obvious, Mages being able to take 40% of your HP in one shatter even with PvP gear, and Rogues obliterating everything in a five mile radius. They should never have gotten access to the Legendaries exclusively in the first place, it's just ridiculous.
When it comes to seasons I'd say S5 and S11. Blizzard failed horribly in terms of Balance in both of these seasons, and I am sure it will continue down the road if PvP stays the same as it is now. We'll see in MoP though.
The most balanced season in my opinion was S7. It was not the most fun, but overall a season where Blizzard actually succeeded in terms of Balance.
They might make my class (Hunter) actually viable for ONCE in MoP. Hunter has always been a class that isn't viable in terms of other classes in MoP, they might score high on the charts in PvE but they're horrible in PvP at max level, you can only make a difference if you heroic PvE trinkets from DS. I mean, look at Hunters representation in Arena and you'll see how horrible it is.
Oh well, post along!