Morale
Morale is a hidden mechanic present in Assassin's Creed II and Assassin's Creed: Brotherhood that determines when enemies will run in combat. Note that the values given below only apply once you enter open combat - assassinating two Brutes will not cause an Agile to run at the initiation of combat, since Morale only applies once enemies become hostile to you.
Morale in Assassin's Creed II
Morale in Assassin's Creed II is handled on a specialty-basis, to wit:
Archers have 30 Morale points Agiles have 40 Seekers have 80 The Prima guide lists Brutes as having 1000 Morale points, though that may be only a way of stating that Brutes never flee unless disarmed. All Guards without specialties have 20 Morale points, regardless of whether they're basic guards or Captains.
Morale for each guard in combat decreases by 5 whenever an Archer, Agile or basic guard is killed, as well as when a Counter Kill, Disarm, or ground-assassination is performed. Disarming an opponent and killing them with their own weapon decreases Morale by 10, Seeker death and pistol-assassination knock off 20 points apiece, and a Brute's death is worth 30 points of lost morale. Conversely, each time Ezio is hit (regardless of the damage he takes), all guards gain 10 Morale, with an extra 25 if he enters Critical State. Lastly, evading guards (so that the edge of your mini-map goes from red to yellow) adds 20 points to the Morale of all guards.
There are exceptions to the above system, however. An enemy who is disarmed will, under most circumstances, run immediately. This can be treated as a -∞ Morale penalty for being empty-handed.