I have always been under the impression that Nemesis were like anything other NPC in any other game--that they were killed when they exceeded their wound threshold, unless the GM spent a destiny point to have them make an escape because they were central to the plot--a recurring villain who wasn't supposed to be killed yet or something.
I just read through Hidden Depths and I discovered I had it wrong. At least technically. The adventure points out that Ironarm, as a nemesis, is capable of surviving past his wound threshold, and, barring specific action taken from the PCs will survive the adventure to optionally haunt the PCs later, unless the PCs take specific action to prevent this from happening (i.e. decapitating his unconscious body). I double checked the nemesis section of the CRB and, yep, Nemesis are like PCs in every regard.
My thoughts are that it might be interesting to, ONCE, bring an NPC back that the PCs left for dead, particularly if they had to flee the scene really fast and there was a plausible means for the NPC to not bleed to death. However, if, as the rules imply, ALL nemesis enemies can do this, the PCs are going to start coup de gracing corpses left and right to make sure there aren't survivors as a matter of habit. You could argue whether or not this is ethical, but either way the GM has put them in a position where the players feel this is necessary, and that should set off some warning lights. I'm of the opinion that if a GM doesn't want to see behavior in game from his PCs, he shouldn't encourage it by making it the 'smart' thing to do.
From the player's perspective, if you can't actually kill nemesis unless you cheap shot them when they're already down (or by a lucky crit), that takes a lot of fun out of the game.
This has been bothering me for days, as this seems like a crap rule to me, both as a GM and a player, and I wanted the community's opinions on how they handled defeated nemeses.