Taken from Syonyx's FAQ @ GameFAQS.com
:
So you want to kill as many Mudokons as you can, do you? Alright, here's what
you do. First of all, get some personal counseling. Seriously. Second, keep
reading.
In order to get the special ending, it's not good enough to just not save your
people. You have to go out of your way to see them dead, so that they go up on
the Mudokon status boards as 'Casualties'. Remember the ones in secret areas,
too. If you just pass them by, all you get is the 'bad' ending. You can speed
through the game awfully quickly that way, though.
Unfortunately, you can't kill absolutely every one of the green dudes, because
you need to rescue a few just to be able to progress through the stages. Here
are the Mudokons you who must escape your vengeful hand:
==> At the very start in Necrum Mines, you must save the first 2 Mudokons
(excluding the ones in the secret area) to open the gates so you can advance.
==> Even before those two, there are 9 Mudokons at the end of the first
secret area that you cannot reach, and consequentially cannot kill. These will
have to simply be left alone to wallow in their despair.
==> The first 2 blind Mudokons you encounter, in Tunnel 4, each have to jump
through their respective bird portals to open the doors.
==> In Tunnel 5, rescuing the first blind Mudokon summons the lift, and the
second opens the door.
==> In the Slig Barracks, Block 2, you have to rescue 3 Mudokons to get the
Shrykull power-up. Otherwise, you can't exit.
==> In the Bonewerkz, Annex 7, you would think that you need to send some
Mudokons through the Shrykull portal to get to be able to get to the exit.
But, if you have at least 2 bones from Annex 6, you can use these to blow up
the mines blocking your way on the very right. QuikSave before you try,
because you have to throw them just right and hit the last 2 mines, then jump
down without falling onto the first mine. If you think you can accomplish
this, go ahead and kill the Mudokons here.
==> In the final Zulag, you have to save 2 Mudokons to get the Shrykull
power-up so that you can finish the game.
Other times, you will need to have Mudokons follow you to work wheels and such
so that you yourself can advance, but you don't have to send them through a
bird portal.
So you are obligated to save only 11 Mudokons, and allow 9 to live unrescued.
The other 280 are fair game. There are many ways to kill them: zapping them,
walking them off cliffs, blowing them up, getting them shot... The fun never
ends. For those Mudokons whose mode of death is not so obviously at hand, you
have the default of slapping them repeatedly until they die. Remember, too,
that if a Mudokon sees another die, he will become depressed, and if he is
already depressed, seeing another Mudokon die will then drive him to commit
suicide. Those crazy Mudokons.
Is this true about the ending?
Please tell me more about "Invincibility" and more about the "Feeco Depot Trick"
Abe's Exoddus 3rd Ending?
Well, now I am at Slig Barracks (I was at Bonewerkz but forgot to save. 
So, go -ddcheat! Yo ho ho. 
