Since patch 3.1 and the changes to Seal of the Martyr/Blood there seems to be a lot of people out there asking themselves what seal they want to run in arena these days. The answer is it all depends what comp you are running.

Seal of Command

Pros
- Auto criticals when a target is stunned or incapacitated
- Scales a little bit better because it gets more from attack power and spellpower
- Hits a bit harder
- Judgements deal more damage
Cons
- Procs about half as often as martyr
- Has a 1 sec internal cooldown with its seal procs
- RNG seal procs

Seal of the Martyr/Blood

Pros
- Procs off every swing
- Scales with Haste buffs
- Saves 1 talent point
- Makes Multiple target Divine Storms do a lot of damage
Cons
- Deals damage back to you mostly with judgements
- Is more RNG with its burst

Before patch 3.1 paladins pretty much used martyr exclusively. At the same time there were not many double dps paladins out there. I was one of them and used seal of command. After 3.1 with the right partner like a rouge seal of command can be great. I find myself leaning toward seal of the martyr these days because healers seem harder and harder to kill. So really it ends up being that seal of the martyr does a little more damage but is to rng for my liking. For 3s comps and healer comps tho I suggest using Seal of the Martyr. In all honesty tho with no outside buffs martyr doesn't do much more damage then command. It all depends on things like Heroism/Bloodlust how much you can stick on your target and how often the target is getting stunned or incapacitated which seal you decide to use.