Here is a small guide that will give a kick start out to people that are not sure how to gem. This will almost always be the case of how you will gem. In rare cases there might be a reason to gem differently, but in most cases just follow this guide and you will be fine.
From this point on when I say main stat I mean the main gem for your class/spec.
Warrior, Paladin, Death Knight = Main Gem +40 Strength.
Hunter, Rogue, Enhancement Shaman, Feral Druid = Main Gem +40 Agility.
Elemental Shaman, Balance Druid, Priest, Warlock, Mage = Main Gem +40 Intellect.
Figuring Out Yellow:
This is one thing that might differ from class to class, yellow. You will use them so rarely but when you do you will have a choice of +20 Critical, +20 Haste or +20 Mastery. I will always suggest Critical and you would be fine if you follow that for all classes but haste or mastery might be better for yours. Using critical for the limited amount you might ever use it won't hurt you however.
How to Meta:
If your main gem in +40 Strength, your meta is Reverberating Shadowspirit Diamond.
If your main gem is +40 Agility, your meta is Agile Shadowspirit Diamond.
If your main gem is +40 Intellect, your meta is Burning Shadowspirit Diamond.
If Red, +40 Main Stat Gem
If Yellow, +20 Main Stat/+20 Critical.
If Blue, +20 Main Stat/+20 Hit Rating.
Gear With One Slot: (not head)
+40 Main Stat, No Exceptions.
Gear With Two Slots:
If no slots are red, +40 Main Stat in both slots.
If both slots are red, +40 Main Stat in both slots. Duh.
If one slot is red and the other yellow, +40 Main Stat and +20 Main Stat/+20 Critical.
If one slot is red and the other is blue, +40 Main Stat and +20 Main Stat/+20 Hit.
Belt Buckle from Blacksmith or Blacksmith Sockets:
+ 40 Main Stat, No Exceptions.
Use three +67 Main Stat gems in place of regular ones.
There you go, nice and simple. All the mystery taken out of gemming, so easy an Orc could do it.
Don't forget to reforge and enchant too, but this gemming is a step in the right direction.