[color:"orange"]Or, for me the best one: if killing them would cause you to have problems, morally.[/color]

There are lots of quest or story related reasons you may not wish to fight/kill someone, but unless the game is balanced to have fewer, more strategic fights, I can not see this being a common situation. Unless everyone started off stating their motive before attacking you, it could be hard to keep track of who was misguided, who was acting out of desperation and who was just greedy or evil.

Fight conversations, or background stories, may be more common in friendly towns, but there will likely be animals, demons, evil wizards, etc that either can not or will not accept any compromise. If the enemy's goal is to wipe out all resistance and kill or enslave everyone, you may be able to bribe, trick, or reason with the odd one, but as a general rule if spotted you would either have to kill or be killed. Though as you say, another option some of the time would be nice to have (especially if there were at least some disadvantages or missed opportunities as a result of unnecessary killing)

[color:"orange"]I prefer a little more moral depth to my massacres.[/color]

I don't mind a little moral depth, but as long as there is otherwise enough story and non-combat quests in a game, I'm fine with straight experience points and loot based massacres.

[color:"orange"]There's no moral qualm in killing something that attacks you once it sees you, until you kill it.[/color]

In DD, there was a group of soldiers which fell under a spell, and would attack you on sight. At first I ran away without attacking back. However, I could not tell the army about the situation or otherwise get any help, so I went back and killed them for the experience points. Had I waited, the mind control would have worn off after encountering one of the mages that cast the spell.

[quest to kill an unbeatable foe, forcing a surrender]
[color:"orange"]some would whine like that not being able to kill him was destroying their freedom of choice, so I'd be inclined to just give him the ability to be killed, but make it near-impossibly hard.[/color]

I was thinking more along the lines of just making the opponent a much higher level. If the quest was near the start of the game, the opponent could have a mid or late game level. Talk now, or wait until much, much later to use brute force.

[opponents that attack and then flee]
[color:"orange"]If it gets annoying, I'd invest in a bow to pick them off as they run away.[/color]

Where possible, that is what I would do. It was really annoying in old console games / ports (like Final Fantasy) that had randomly generated encounters as you walked around. You could get the combat intro, then wait for the game to set up combat, then have some weak opponent run away, then get the stats screen showing you got zero experience and loot, then get the combat extro and return to the regular environment. Even some newer games (though none recent, that I know of) can have similar random encounters.