You should have named this topic @Dilbrt lol My primary profession is healer and I'm a master Jewelcrafter, meaning I have every rare gem cut in the game (AH, Rep, and Halaa) plus 12 Hyjal epic cuts. I know a couple things about gems.
As I say with the question of trinkets, it depends what you need. Feel free to armory my guy and see what kind of gems I use, however I can save you the time and tell you what gem I use for what color slot. I will not be including the epic gems you get from heroics or pvp because you can only have one of those so they're not worth spending much time on.
Blue = Royal Nightseye (9heal,2mp5). Heal + mp5, everything a paladin could hope for. A lot of the higher tiers are loaded with blue slots and this is what goes in it.
Red = Again, Royal Nightseye. Now I do have a single +26 healing gem in my shoulders but that's just so I could make myself feel that it was worth becoming a jewelcrafter.
Yellow = Now this kinda depends on the rest of your gear. If you need crit, stick some gleaming (8 spell crit) in there. If you're fine on crit, stick some luminous noble topazes (9heal, 4int) in there.
Things to stay away from:
-Brilliant Dawnstone (8int): This does so little for you that you're throwing away a perfectly good gem slot. If you need crit then stick gleaming in here. If you're that hard up for mana then probably you've done something very wrong with your gear and this gem won't help you.
-Teardrop Living Rubies (18heal): 1st off they're very expensive, even to me as a jewelcrafter. Second if you do nothing but load up on +heal you will be nerfing something else so much that your overall gear will be in poor shape. Multi-colored gems are a good thing, use them.
-Lustrous Star of Elune (3mp5): This is only 1 mp5 less than a nightseye and you're missing out on some healing.
-Sparkling Star of Elune (8 Spirit): One would think I wouldn't have to include this, but I've seen a paladin that used this. Spirit isn't worth your time, get mp5.
One final note. Don't forget there is also Dazzling talasite (4int, 2mp5). I wouldn't reccomend it for normal gear, but if you're trying to activate a certain meta (ie. mystical skyfire) then keep this in mind. I would avoid it unless you needed it though.
As for PvP gems:
-You do not need any mp5, matches (specifically arenas) won't last long enough for it to be worthwhile
-Lots of Spell crit gems
-Stamina gems
- +healing gems
-Can't forget resilience gems