When it comes to morale, I generally do the following:
Improvise on the Fly: Like Tim, I usually just make a decision while the action is happening.
Roll Dice: On the rare occasions when I use dice to determine morale, I just roll a d6 and make up my target right before I roll. An example: Things going bad for the orcs? They'll surrender with a roll of a 1 or a 2, run away with a roll of 3 or 4, and fight on with a roll of 5 or 6. Easy peasy. No tables. No fuss. And it only takes a second. I've never actually used a morale table from a ruleset.
Create Thresholds: On a few occasions, I have set certain thresholds by which a creature or NPC will run, surrender, or otherwise give up the fight. Maybe it is a percentage of hit points. Maybe it is a percentage of creatures who die. Once the threshold is hit, the creatures or NPCs try to find a way out of the encounter. I base this approach on Mutual of Omaha's Wild Kingdom--when the lions and hyenas meet, they usually do not fight to the death. They fight until dominance is established and the other party runs away.
The reality is that I never think about it in terms of "morale;" I think it about it terms of what a creature or NPC will do in an encounter. I have run encounters where I have used more than one of these approaches. I am a pragmatist when it comes to gaming. Whatever works and adds to the session is the direction I go.
When it comes to morale and running an encounter, what works for you?