My experience has been that in general, Holy will give more healing throughput than Discipline. However, on many fights Discipline gives "enough" healing. Other than Lich King where the mechanics make shielding far superior, the primary benefit of Discipline is that it provides a better tank cooldown. When you need to prevent a tank from dying, Pain Suppression is flat out better than Guardian Spirit, and you want the first priest in your raid to be Discipline in these situations. Good examples would be hard mode versions of Saurfang and Putricide.

If that's not the case, Holy is probably a better choice. Holy is definitely better on any fight with a constant AoE damage pulse (because of the 7 second Prayer of Mending), and it's also better if you have Val'anyr (though don't let that stop you from speccing discipline for a fight that demands it).

I strongly disagree with the CD sentiment here. PS is a relatively weak reactive tank CD because it only increases the tank's current HP which is low in emergency situations. GS will not only make the tank survive the next melee hit but the subsequent one as well from its 35Kish heal.
PS is better as a proactive CD for predictable periods of high damage, festergut being the best example.
Regardless neither is a deal breaker (or maker), and considering every paladin has a longer lasting version of PS, that's not a big surprise.

I'm talking about proactively using a tank cooldown at a scheduled event. For example, on hard mode Putricide, we have a DPS spec warrior in mostly DPS gear tank the boss for a bit during phase 3. He gets a pain suppression when he's at full health and then taunts. Just before pain suppression wears off, he uses shield wall. And the next tank in rotation taunts off of him before the shield wall wears off.

That type of strategy simply isn't possible using Guardian Spirit. Yes, Guardian Spirit has a shorter cooldown and is more effective against people low on health. But if the tank knows in advance that he needs another Shield Wall, then Pain Suppression is flat out better than Guardian Spirit. Guardian Spirit will trigger once preventing their death, and then the tank will die three seconds after that.

Other situations where you know in advance that you'll want a Pain Suppression include later stages of Festergut tanking and Saurfang when he's high on runic power with several marks in the raid.

I agree that if you're just interested in a random button you can press to prevent someone from dying, Guardian Spirit is better than Pain Suppression.

If it's the abacus, I don't usually use that for any progression fight. Just wading through heroics and early raid bosses and such. I generally use a regular Solace, having had no luck with the heroic one dropping. I also still need a token for the gloves to get the 4pc T10, since it was changed to actually be fairly strong as opposed to totally useless. My gemming is also somewhat scattered, depending on what I was feeling short on at the time. Definitely room for improvement still.

Thank you so much for the responses. They have all been helpful. It does look like I need to go to a more renew-centric spec, so I'm going to switch over to that this week. What are your thoughts on dropping Serendipity (3) in order to pick up Improved PW:S (3)? My thinking for this is with points in Body & Soul, a glyphed Imp PW:S would be nice for Shroud of Sorrow and Pact of the Darkfallen on BQL, Gas Cloud on Putricide, Mutated Infection on Rotface, etc. This would be the resulting spec: Renew Centric Holy Spec

Another question I have also, and this may be a stupid one, but... if I'm going to be casting PoM, CoH and Renew (all instant cast spells) what value do I get from having more haste?

More haste reduces your global cooldown on renew, but not on CoH or PoM, since their cooldowns are set. To take advantage of haste you need to cast your renew non stop and even if you stop for a second, all that benefit you gained from global cooldown is lost, since it's so little. Of course, you have to move for so many fights and I guarantee you can't focus on non stop casting at all times. When you need to cast something long, like flash heal or PoH, with the right stacking of Serendipity, you don't really need that much haste. Yes, it is nice to have and your tier gear has plenty of it, so I personally gem for crit instead and find it way more beneficial for both specs.

I mainly play as discipline raid healer, but my second spec is holy. Same thing for discipline, you need non stop shield casting to take advantage of global cooldown reduced by haste and crit aids your Divine Aegis talent.

More haste allows you to get renew up on more targets during fights like BQL. You do mostly stand around casting non-stop on that fight. My activity on that parse was 99.8%. 30% haste literally allows me to cast 30% more spells during that fight. It's also very beneficial when you go into the air phase and want to cast 2-3 PoHs back to back, because you need to drop that throughput NOW. If nothing else, it's more beneficial than crit, which is realistically the only other option. As a clarification, it does reduce the GCD on PoM and CoH, just not the cooldown. So it allows you to get off the CoH GCD to get your next renew out faster, but it doesn't allow you to CoH any more often.

On other fights, haste can be useful for different things. On Rotface, it allows you to get to casting PW:S to sprint people more quickly, since you were likely coming off some GCD. That's helpful, if not game-breaking.

Imp PWS would be nice, but I don't think it's worth dropping Serendipity for it. Serendipity lets me drop 60k healing in 3 seconds during the air phase. I don't boost people during BQL. Pact is easily healed by a CoH and some PoM bounces, on top of whatever raid healing was already on them. Shroud doesn't require the person to move any faster, that would just spread the fire over more of the room. For Rotface, by the time the shield is consumed, the disease has generally been cleansed anyway, so they're not really taking that much damage. In the end, I need really fast PoHs much more often than I need slightly bigger shields. The one mitigating factor there might be that in taking imp PWS, you could get to mental agility, and since we're casting almost exclusively instants these days, that could be a big savings. But then, I realistically never have mana trouble, and I'm already gemming mostly for throughput rather than regen. And you'd then have to drop some other talents to get MA, which would definitely eat into your throughput. In the end, I choose to spec to emphasize what holy's good at, not to try to cover the times we're caught casting unusual spells.

This is dependant upon your raids' healing set up. As the full time disc priest in my guild, my shield will always be much more superior to that of my holy priests'. My raiders are expected to not need a crutch to move out of fire, especially at the loss of higher damage mitigation. In the strange instance of having no resto druid or disc priest, go for it, you're helping yourself then and the stand in fire people.

Also, haste has been greatly discussed in depth in Squeaksters 'On the Value of Haste'.

Looking at entire fights is misleading. In my book, the periods of time that do matter are the ones where you are nonstop casting - otherwise they're not challenging per definition. Which challenging fights are you thinking of where you are not chain casting in the "interesting" phases?

Regarding the effect of PoM and CoH cooldowns interfering with haste, see the haste thread, specifically this post: On the Value of Haste. If you have additional material to share regarding your assertion that "So for the majority of the currently relevant encounters the stacked haste is almost completely wasted", please do so. The math has been done, but simulation results would help.

I don't see how the fight is challenging if you can afford to stand in one spot the whole time and cast non-stop. We are not talking about moments when you stop healing, just because there is nothing to heal, but rather when you have to avoid certain gimmicks of the fight, which require you to stop healing.

I'm not talking about BQL, it's far from challenging especially for healers, heroic or not. How about heroic Sindragosa? It's a prime example of holy healing, because disc is garbage for it. You don't cast as much when you get the debuff (especially in the last phase), you don't cast while getting pulled in (you can restart when you are running out though), you don't cast while in ice blocks or during transition phase. Heroic Putricide? You don't have to stop casting, but there is so much multitasking, like watching the plague, moving from goo, stacking together, spreading out... I can guarantee that you can not possibly cast non-stop during all that, you stop now and then at least for a second, and there goes your haste (since we are talking about fractions of a second). Do you really think you can save someone with your crazy haste renew spam at the prime time of the fight? Holy is not the spec for it, disc is. So not taking the whole fight into consideration, while talking about holy priest is not right either. Summary: you stop casting for a second or two far more often than it takes you to gain that time back with a little advantage of haste you have.