A: Fortitude, Life Force
B: Onslaught, Immense Power, Harmonize
C: Iron Wall, Proficiency, Divine Speed

Fortitude gem, once activated, "takes" all incoming damage until 100\130\160 damage is taken, or until 20\15\10 seconds pass.
Life Force gem, once activated, recovers 80 health over a 5-second time period.
Onslaught gem, once activated, increases Cross Gauge gain in all conditions by 20\40 percents for 20\15 seconds. There are no level 3 Onslaught gems.
Immense Power gem, once activated, increases damage output by 10\20\30 percents for 20\15\10 seconds.
Harmonize gem, once activated, immediately recovers 60 health.
Iron Wall gem, once activated, reduces all damage taken by 10\20\30 percents for 20\15\10 seconds.
Proficiency gem, once activated, saves 10\40 percents of used Cross Gauge during 20\10 seconds period. There are no level 2 Proficiency gems (Not counting DLC and Xbox 360\PS3 gems).
Divine Speed gem, once activated, increases walk speed by 10\15\20 percents for 20\15\10 seconds. It does not increases attack speed, jump height or jump length.

Fortitude gems, when activation conditions are correctly chosen, may give up to raw +100 health bonus per gem to your char, so Akuma with 3 Fortitude gems can be as tough as Hugo! Try these conditions: get hit by 2 specials, get hit by 4 normals, your partner connects launcher (for sub and only if you actually use launchers as main).
Life Force gem provides slightly less support than Fortitude, but its bonus is easier to receive as you don't have to take any damage during its activation period.

Onslaught can turn any char you wish into a battery, especially when you put your battery as main and give him\her two gems that activate once your partner connects with launcher and you do, so you can juggle launcher into launcher and have both gems activated at once, building meter nearly twice as fast for almost 15 seconds.
Immense Power can help with damage output, but it can be totally negated with Iron Wall. If you don't want to turtle with Fortitude and want to rapidy strip your foe off some HP, go ahead and pick it. Just make sure its bonus exceeds the bonus from Fortitude: you'll have to cause at least 500 unmodified damage over 15 seconds with level 2 Immense Power gem so that its bonus would suffice.
Harmonize gives 60 HP instantly, but it's unlikely that you'll get hit by 2 specials in the end of round rather than in the beginning, so Life Force is a direct upgrade. Note that it does not increases amount of recoverable HP, much like Life Force!

Iron Wall gem reduces all taken damage while it's up. You should take 1000 damage over 20 seconds or 500 over 15 to make it strip 100, like Fortitude gem would, what is unlikely if you are not playing in competitive where people actually can do that much damage with cross assaults. And level 3 gem activates on Pandora, which is rarely used at all. Gouken, Evil Ryu, Akuma and Gen would say "no use".
Proficiency gem does not allows you to use meter-consuming stuff without having sufficient amount of meter (for e.g. you cannot use EX when you have 90% of one block and level 1 Proficiency gem activated), only saves some for further use. The only case where it'd be more useful than Onslaught is when you burn all 3 blocks.
Divine speed only affects walk speed. If you use a fast char like Chun-Li or Cammy, you can probably walk backwards to make your enemy whiff attacks, but it's not too useful otherwise.

Life is crucial, and extra HP is really helpful when fighting highlevel enemies, not when dominating 0 BP noobs that can't even block - these 200 HP from two Fortutude gems can let you survive and come back with all your meter. Meter gain is rather important, providing you can put it in use, but if your chars do well without that extra meter you can have with these gems, use some health instead. Extra damage and damage resistance generally nullify each other and themselves (when both chars are at 10% damage bonus, they are quite even), but when you have Immense Power popped up, you may decide to use some meter for extra damage, so it's of higher tier. You may use gems that fit your playstyle - for example, you may play with battery Heihachi or Balrog with some Fortutude and Onslaught gems to gain a lot of meter, and then tag Akuma, Juri, Ogre or other high damage and meter hungry char via Launcher (boost combo or juggle starter should do the trick) so that this char's gems that activate when partner connects with Launcher pop up.