Gemming is fairly straight forward for moonkins. Gems are usually dictated by your current stats and the color of the gem socket.
Meta: Always use the Chaotic Skyflare Diamond.
Blue: You will want to only use two blue gems to activate your meta. You should be using SP/spirit gems, and preferably in blue slots only.
Red: Red slots should always, always, always be pure spell power gems.
Yellow slots: Yellows change a bit depending on your caps. If you are not hit capped, a SP/hit, or even a pure hit gem, will be the best to equip. If you are not haste capped, then haste is what you should focus on. After your soft haste cap, which is very easy to reach these days, you should gem yellow slots with SP/crit, if the socket bonus gives you +5 spell power or more. Once you have covered your soft crit cap, because of the slight favor to haste, SP/haste gems becomes the better choice in yellow slots.