Twilight Zone: Depends on tactics used. If I recall correctly, the strategy my guild used had Vesperon and Shadron up in the same time. When Vesperon is active, the raid takes damage from twilight torment. That is also the time when Sartharion's breath hits the most. You can position yourself so that flame wall coming from one side doesn't require any movement and if it's coming from the other, you have well over ten seconds to move. Shadow fissures are harder to dodge, though, and require better reaction time than otherwise.
Malygos: Unless something unexpected happens (such as Malygos gaining the spark), DPS-increase for phase2 transition.
Ignis the Furnace Master: When molten construct is active or if situation looks bad (such as one of the healers getting silenced by flame jets)
Razorscale: Either used as DPS-cooldown while she is grounded, or when she lands. Possible to use on last ground-phase so that you use it for both purposes.
Heartbreaker: As a DPS-cooldown to kill the heart in case the raid lacks DPS, used during Tympanic Tantrum, or if there's multiple life sparks active
I Choose You: Steelbreaker: After Brundir and Molgreim are dead, duh
Kologarn: If a healer gets gripped, when rubble earth spawns
Auriaya: The pull. If a sentry gets loose and attacks you, you might even survive with the increased armor.
Hodir: Frozen Blows after flash freeze. If you fail to move away from Icicle, the increased healing power easily makes up from that. By timing it after flash freeze, you don't have to worry about running to snow.
Thorim: The end of the encounter (damage ramps up over time). If you start the fight in tunnel, that might also be a good time to use it, seeing the cooldown should finish by the time you need it again. You might need to shift out on lightning charge.
Knock Knock Knock on the Wood: If a healer gets silenced by Ground Tremor, when detonating lashers start exploding spawn, the end of the encounter. In the last case you might have trouble if you move individually rather than everyone stacking at one spot and then all moving when bombs appear.
Firefighter: Phase2, especially if the group of players you are assigned to heal (I believe assigning groups to heal was a common strategy before nerfs) is targetted by rapid burst multiple times in row. If you are still shapeshifted when VX-001 casts Spinning Up, you might want to shift out from tree in case the barrage comes from a bad position. Same goes to frost bomb in case it lands near you and fire prevents you from using a straight route away. The cooldown should finish by phase3, in which I'd use it again if a healer dies, is out of range from tanks or such. The same thing than before applies to laser barrage and frost bombs, though, and you might need to shift out.
I Love the Smell of Saronite in the Morning: Shortly after Animus spawns (so that ToL lasts until it dies).
Yogg-Saron: Phase1 if someone decides to spawn a lot of guardians. Otherwise Phase2 to help DPSing the tentacles, unless you can get to phase3 so fast that the cooldown doesn't finish. In case of Alone in the Darkness, you could either save it till the last moments of the fight or if Immortal Guardians happen to get healed.
Algalon the Observer: Used on demand if healers have to move from cosmic smash (I've had so many wipes on him because tank-healers moved and didn't announce it. If other healers don't have to move, you probably don't need to, so speed reduction doesn't matter in that case, either), or in case two stars explode soon after each other. If you have bad luck with positioning of cosmic smash, you might need to shift out. If cooldown is available, phase2.
Beasts of Northrend: The point where there is six stacks of impale. You could also save the cooldown in case of bad managment of bile and poison, or to the point where second worm enrages. If you use ToL during Gormok, it should be up for Icehowl (in which it probably is best used to get extra DPS when Icehowl is stunned).
Lord Jaraxxus: Probably best saved to unexpected situations such as two mistresses being up. Running away with legion flames shouldn't be an issue even with speed reduction.
Faction Champions: The beginning of the fight when healing is at its highest. Increased armor also reduces your threat towards melee champions, probably making them leave you alone.
Twin Val'kyrs: Probably best used during vortex of your own color (when you don't have to switch) when other healers are moving and players are moving past designated soakers and might thus be hit by the orbs (at least my guild used a strategy of having specific players soaking orbs of their color in specified areas on hardmode).
Anub'arak: Phase3 after the initial moments when everyone's health is still dropping low. Instant regrowth sounds pretty damn nice for healing penetrating cold targets..
Lord Marrowgar: Should be used either when other healers get spiked or during bone storm (during which armor also reduces bone storm damage, doesn't it?)
Lady Deathwhisper: Phase2. You might want to wait a situation in which a healer gets mind controlled. If DnD appears on top of you or multiple ghosts are chasing you, you probably want to shift out.
Gunship battle: Very nice if you are doing I'm on a Boat, after Muradin/Saurfang starts getting 20 stacks or so. Otherwise you can use it to... look cool?
Deathbringer Saurfang: The end of the fight.
Rotface: Probably best used when other healers have to move (meaning that you probably don't have to at that moment).
Festergut: After third inhale so that ToL still lasts first moments after Pungent Blight. Dodging malleable goo shouldn't be an issue.
Professor Putricide: Last moments of phase3. Seeing that Professor is slowly dragged ahead of slimes, the speed at you move at which doesn't matter much. You require faster reactions with malleable goo, but you still should have the time to move away from it. I also believe that in hardmode it is common that DPS-player juggle unbound plague between themselves (at least that's the way I've done it) so that healers don't have to.
Blood Prince Council: In my limited experience the damage is greatest when Taldaram is active. If you get targetted by empowered flames, you might want to shift depending on circumstances.
Blood-Queen Lana'thel: On air-phase or used on demand if healers get Pact of the Darkfallen. Judging my limited experience (from 10-man heroic mode) the raid-damage is actually easier to heal after last set of bites due to vampire's self-healing, but in case that's not the case in 25-man, ToL probably should be used here. Swarming Shadows shouldn't be an issue to handle even with speed reduction. If you get pact, you might want to shift out.
I can't comment Sindragosa or Lich-King because I haven't done those encounters.