Hey guys, sorry for being absent from this thread for the past few weeks (more like months). Have been kinda busy lately with exams and VP capping...
Anyway, the guide has been updated for patch 5.1! Check the OP for the RED parts. I also took the time to answer to most of the questions in the thread that I hadn't had a chance to do so far.
You should check WoL to see for each fight which spec achieves the highest dps.
weapon>trinkets>chest>pants>helm>shoulders>gloves>boots>belt>cloak-neck-rings>wrists (because wrists are 502 only)
If you are lazy though, you can use this AWESOME site: http://wowupgrade.com/
Remember that your 2nd upgrade is always most effective than your first (1/2-->2/2 > 0/2-->1/2)
a) You won't need to disengage anytime soon to avoid X damage.
b) You won't get hit by anything else by disengaging (maybe there is some hot lava behind you).
c) You are not all stacked up going through a burst healing phase, because you jumping backwards will mean that you will not benefit fully from the aoe healing that is going on at that moment, so you will end up getting less healing overall.
Of course, I will still take that glyph since there is an opening with the Marked for Death getting removed, and well... we don't really have anything else to take.
They mostly matter for BM hunters, since you might want to wait (5 seconds max) for some internal cooldown to reset before using your BW.
As for Survival, on an extremely tight enrage boss (like Gara'jal was at the start), you can wait to use your Rapid Fire when you get your Bottle of Infinite Stars proc + pot to maximize dps. Of course always being careful that you don't end up using 1 less Rapid Fire overall due to waiting too much.