Isn't morale now mentioned as being part of "hit points"?
3E definitely still had morale as a condition. Shaken, Frightened and Panicked where 3 "morale" conditions.
I didn't like any rules that used Will Saves against fear or morale effects. Or maybe I should say I dind't like that Fighters and Barbarians had low will saves? These guys go toe-to-toe with Dragons! They should have the best chance to shrug off these effects!
Good point. One could build the rule such that you use Will or Fortitude, whichever is higher for saves.
The real objective of morale rules is to model the psychology of a soldier in a losing battle. For a newbie DM, that means realizing that if YOU know the orcs are losing and the PCs are going to win, then the orcs probably know that as well, and would probably run.
If I were making a 3e morale rule, I'd look up the Intimidate skill, the Shaken, Panicked and something else conditions and the 2e/1e morale rules. I'd make sure the 3e morale-like stuff meshes in with the rule verbiage.
I'd prolly make it a d20 role versus a base value of 15, and give a modifier for the side that has more units, and modifier for "looks like we're losing". Then I'd set conditions on what triggers a morale roll.
Basically, make it something I could roll every turn, without it coming up as a retreat until it was obvious the enemy should run.
Honestly, I'm not sure if a saving throw (i.e. level) matters in a morale check. A char should run because the situation is looking like his side will lose and HE will die. A 15th level NPC who just saw half his evil party die, including his leader versus a PC party of 15th level would probably be wise to run away.
Some modifier ideas:
-1 you leader is dead
-1 you are outnumbered
-1 you are outpowered (enemy side has more HD/levels than your side)
-1 enemy successfully Intimidated you
-1 others have failed a Morale check
-1 you are Shaken
-1 you are Panicked
-1 you are in Fear
+3 you are a zealot
I just made that stuff up, assuming I got the right conditions, etc. The real point though is, if the NPCs are losing, they should probably run.