Pretty much everything stacks. Abilities that don't stack tend to be fairly obvious, such as justicar, shaman, and druid's spell power->attack power passive, for the obvious reason that 3x attack power would be overpowered.
Even a lot of abilities that I think wouldn't stack or would share the same CD don't. For example, both the shaman's and druid's spell to return 10% of mana each hit are on separate cooldowns, even though they are the exact same ability. Purifier's shield and druid's shield are also on separate CD's.
The only ability that I've encountered that hasn't stacked that seemed liek it might is the warden's two orb spells.