Ghostcrawler has mentioned several times that Blizzard is trying to constrain mana regeneration for healers, in order to encourage healers to heal more efficiently and more thoughtfully. For the most part, Blizzard has failed in this task. The 3.1 changes haven't really had much effect on mana concerns.
There is one fight in Ulduar where mana conservation becomes vital: General Vezax.
Vezax has an ability called Aura of Despair which shuts down pretty much all mana regeneration for casters. No Illumination, no mp5, no spirit, no Replenishment, etc. The only way casters can regenerate mana is by standing in pools of saronite vapour every so often. However, the vapour damages you as it returns mana. Hard-mode for Vezax involves not using the vapour at all.
In our first attempt on Vezax, I tried using the vapour, but managed to kill myself while only regenerating 600 mana. I'm still not 100% sure what happened there, but I chose to ignore the vapour for the remaining attempts.
Vezax was the most fun I've had healing in a long time. It's so good to watch overhealing once again, to heal carefully, to predict damage and use cooldowns appropriately, rather than spam madly. Almost all the raid damage in the Vezax encounter is avoidable.
But the lengths the fight had to go to create that dynamic. No regeneration at all. Entire stats and talents become useless. Blizzard's tiptoeing around for the rest of game, cutting the effect of spirit by a few percent, or nerfing Illumination, none of that had the effect of simply saying, "No Regen."
I still think that mana is the best resource for healing. I've played games that use an energy-like system and--while energy is great for DPS--it just isn't as good as the gameplay involved in healing while keeping a careful eye on a dwindling mana bar.
It's too late for WoW, but I think that future MMOs based around the tank-healer-dps trinity would be well-served by taking a cue from General Vezax and simply not allowing healers to regenerate mana in combat. Give them talents that add extra effects, or do new things, but close the door on regeneration permanently. It seems to be the only way to prevent healing from falling into the mindless spam routine.