I'm going to borrow a little of the math Exavier did in this thread, but I'll try to keep things easy to understand. Let's first start by examining Seal of Command:
Seal of Command
Gives the Paladin a chance to deal additional Holy damage equal to 70% of normal weapon damage. Unleashing this Seal's energy will judge an enemy, instantly causing 228 to 252 Holy damage, 456 to 504 if the target is stunned or incapacitated.
Now let's put SoC on a well-geared Retribution spec Paladin with the following stats:
800-1000 damage (paper doll slot)
Weapon Speed: 3.6
Seal of Command damage range: 560-700 (average 630)
Ah, but SoC has a 29% spell coefficient (meaning 29% of your spelldamage is applied to any SoC proc). Plugging that in, we get: 29% of 350 = ~102
Seal of Command damage range: 662-802 (average 732)
So on average, with these stats, we can expect SoC to deal 732 damage on each proc. We also know that the proc rate on SoC is 7 per minute. Let's plot this out over the course of a minute to see how much damage we do with SoC.
SoC Damage Formula: (Average Proc) * (Procs per minute)
(732) * (7) = 5,124
SoC Critical Damage Formula: 2 * ( (SoC Damage) * (Crit Chance / 100) ) = SoC Critical Damage
2 * ( (5,124) * (.3) ) = 3,074
SoC Damage Total Formula: ( SoC Damage - (SoC Damage * Crit Chance) + SoC Crit Damage ) = Total SoC Damage
( 5,124 - (1,537) + 3,074 ) = 6,671
Keep in mind that this doesn't take into account any other skills, talents, resists, mitigation, etc, so this should only be used for comparison purposes. Now let's take a look at Seal of Blood, using the same stats for our Paladin.
Seal of Blood
All melee attacks deal additional Holy damage equal to 35% of normal weapon damage, but the Paladin loses health equal to 10% of the total damage inflicted. Unleashing this Seal's energy will judge an enemy, instantly causing 295 to 325 Holy damage at the cost of health equal to 33% of the damage caused.
Seal of Blood damage range: 280-350 (average 315).
From this we can see that although each SoB proc hits for less than an SoC proc (315 vs. 732), SoB procs on every swing, not just 7 times a minute. Let's plot out the damage done over a minute as before, but using SoB this time.
SoB Damage Formula: ( Average Damage * (Total Seconds / Weapon Speed) ) = SoB Damage
( 315 * (60/3.6) ) = 5,250
SoB Critical Damage Formula: 2 * ( (SoB Damage) * (Crit Chance / 100) ) = SoB Critical Damage
2 * ( (5,250) * (.3) ) = 3,150
SoB Damage Total Formula: ( SoB Damage - (SoB Damage * Crit Chance) + SoB Crit Damage ) = Total SoB Damage
( 5,250 - (1,575) + 3,150 ) = 6,825
So where are we at? Seal of Command does 6,671 damage over a minute, compared with Seal of Blood's 6,825. Not much of a difference, eh? Let's see what happens if we were to Judge each Seal when it was up (and to be fair, the target will not be stunned or incapacitated) in the same 1 minute period. Both Judgments also have a 43% spell coefficient, so we will take our Paladin's spelldamage into account.
JoC Damage Range: (228-252) + (.43(350)) = 379-403 (391 Average)
JoB Damage Range: (295-325) + (.43(350)) = 446-476 (461 Average)
Judgment Formula : (Average) * (Total Seconds / Cooldown) = Damage
JoC: (391) * (60 / 8) = 2,933
JoB: (461) * (60 / 8) = 3,458
Judgment Critical Formula: (Damage * Crit Chance) = Critical Damage
JoC: (2,933 * .3) = 880
JoB: (3,458 * .3) = 1037
Judgment Total Damage Formula (Damage + Critical Damage = Total Damage)
JoC: 2,933 + 880 = 3,813
JoB: 3,458 + 1037 = 4,495
Now let's add the damage from the Seals and their respective Judgements together and see what we come up with:
Command: 6,671 + 3,813 = 10,484
Blood: 6,825 + 4,495 = 11,320
Seal of Blood wins by a margin of 836 damage, which works out to be around 7% more damage.
So what can we take from this? Is Seal of Blood the winner? Well, most of the time, yes. Seal of Command scales with your spelldamage, so past a certain point Command starts to come out ahead. However, Seal of Blood tends to scale better with gear that buffs your strength and crit rating, two stats that Retribution paladins need in spades to do well. Blood also costs less mana to use, but remember -- it deals damage to you with each hit or Judgment.
Certain combinations of high level gear, talents and spells will give the lead back to Command. For example, the 4 piece Justicar Battlegear bonus increases SoC's damage by 10%, and Judgment of the Crusader on the target effectively grants you additional spelldamage.
Which Seal you should use depends on the situation: since SoB procs every swing, the damage is far more reliable, but it doesn't hit as hard as SoC, and it deals some damage back to you. In general terms, I'd say that SoC is better for PvP and SoB has the edge in PvE, but in reality both seals deal a comparable amount of damage.