Notoriety, Weapon, Weapon Level, Weapon skills/attacks used.
Skill points assigned to the skills/attacks.
Skill points assigned to passives (other than the basic skills/attacks).
All of the above will vary # of reps, and how hard it is to defeat an enemy.
Reputation Guide:
http://www.piratesonlineforums.com/f...ead.php?t=6926