Rawr plays WoW better than any one ever will. It takes a perfect scenario and tells you the outcome, so don't take it for fact. Experience / Raid comp / Encounter determines the gems and enchants that best suit your needs. But since you probably can't regem, enchant your gear, and change the raid comp every boss, I recommend the following gem selections:
30 stam in blues
10 agi + 15 stam in reds
dealers choice when it comes to yellow (10 def + 15 stam, 10 hit + 15 stam, or 30 stam)
The gems are just a bonus to your gear. If you chose full stamina or full agility with ~20 gem slots, the difference is ~10k hp vs ~10% dodge raid buffed. You choose.