For fights where there isn't much strong pulsing raid damage, you should use battle stance. If you know that a raid wide damage burst is about to happen, switch to berserker, then switch back to battle after the damage goes out. Using MSV as an example, these are good times to do the new stance dance:
Stone Guard: When Overload is about to happen. If the healers are good, you can also just stand in Amethyst Pool and stay in Berserker Stance
Feng: Epicenter, Wildfire/Draw Flame stacks, Arcane Velocity are all good Berserker Stance times, but mostly dependent on healers keeping you up. Stay in Battle and avoid mechanics if you're afraid you'll die.
Garajal: If you are Voodoo Dolled go Berserker, otherwise Battle Stance
Spirit Kings: First king when you have to stack on tank go Berserker. Should remain in Battle afterwards
Elegon: If you have DBM or another raid warning addon, whenever the add is 25% and about to explode you should be in Berserker. Otherwise Battle.
Will of the Emperor: Battle Stance for the entire fight. Could test if Berserker during Titan Gas is worth it.
Berserker rage is a DPS increase anytime you're losing more ~2% of your health / second. That means always switch to it when DoTs are on you, and switch back and forth in anticipation of mechanics, like the above poster is saying. Don't just stick to the idea that you're "good" as battle stance in a certain fight. Whenever you take noticeable damage and weren't in zerker stance, you lost potential DPS.