Well, seeing how most orcs weren't too bright on the side of masterminding their own schemes and/or organising themselves into any kind of societal structures other than their usual divisions/tribes, I would assume that they would be slowly picked apart and hunted down. However, there is also a good possibility that the Haradrim, Easterlings, or any other such "bad guy group" in Middle Earth could have either dominated the orcs or worked with them. Then it would only be a matter of if and when said groups would dispose of the orcs themselves or they were defeated themselves.
Only my speculation though... good question.
Here is also a site that discusses this question a bit... actually it kindof contradicts what I said a little bit [img]smilies/smile.gif[/img].
http://pub89.ezboard.com/fbree72204f...opicID=7.topic
~Scott