I've been putting together a compendium of all things shadoo over the last few days for a standalone page on the blog, which has taken far more time than I thought so rather than neglect the blog, I thought I'd plagiarise a section from it on proper use of cooldowns. There is no absolute answer here, use your common sense, for some fights where there is an enrage or similar, but for 'normal' circumstances this is the general guidance:
Dark Archangel gives a dps boost as well as mana, the timing of its use is entirely situation dependant. If there is no danger of you running out of mana, pop it as soon as you have five stacks of Dark Evangelism and reuse it immediately it comes off cooldown. If you are in danger of mana depletion, use this at around 80%
Shadow Fiend similarly to Dark Evangelism, this gives a reasonable DPS boost, and should be used as soon as possible providing you do not need the mana, should you need to extend your mana casting it at around 80% (not at the same time as Dark Evangelism)will ensure you don't waste any regen.
Mind Blast has been relegated to a buffing spell since 4.0 it doesn't do enough pure DPS to warrant normal rotational use, it does however provide you with a nice buff, Empowered Shadow, giving you 15% extra shadow damage, you should use MB whenever you have one or more shadow orbs up and the buss has, or is about to expire.
Dispersion is primarily a panic button spell, use it to stay alive. It also returns mana with the drawback of rendering you incapable of doing any damage for its duration, if you have to use it for mana, try and make sure all of your DoTs are renewed before casting it.
Shadow Word: Death makes it into this section because it has an artificial cooldown of sorts, you should only use it in normal rotation if you're running low on mana and its glyphed (it should be). Else it should only be used on a mob under 25% health, and not if it'll kill you.
Hymn of Hope & Divine Hymn should be used sparingly, if at all, they have long cooldowns and are purely situational, have them on the cast bar, but only use them if your party is in dire straits on the health or mana front
Class specific cooldowns (beserking for trolls) give a big boost, in my case haste and should not be ignored, usual rules apply on the situation, else it's as early as possible, try to combine beserking with other damage buffs as the increased haste gives a good multiplier.