While doing research for my own writing, I stumbled across a few articles:
Fictional Geneva Conventions - TVTropes
Useful Notes: The Laws and Customs of War - TVTropes
Convention on Certain Conventional Weapons - Wikipedia

I knew a general bit about Geneva Conventions and what kinds of weapons and conduct aren't allowed in war, but it's easy for me to forget about all that when thinking about settings like this (or Team Fortress 2 or Starcraft) where "shooting the medic first" is just simply the most pragmatic strategy, war crimes be damned.

Granted, as the Equestria Divided setting owes a lot to the Warhammer 40k verse, war crimes are gonna be pretty commonplace and there's no "neutral power" governing conduct in combat. I also imagine fighting a force like the Cult of Laughter (which routinely tortures, maims, and crosses all sorts of moral lines) would quickly cause any other force to abandon lawful conduct and aim for brutal pragmatism.

That said, we know each faction has rules (usually governing what gruesome fate happens to traitors/heretics, but work with me). Is there possible there's other rules of wartime conduct that other factions or particular types of units would have to be pushed very far to break? Would a Stormwing Hoplite have a sense of honor that keeps them from any sort of "cowardly" or underhanded tactics? Would the buffalo tribes have deep-rooted traditions (like not wearing certain types of armor) that most still aim to hold true to even in times of war? Heck, even members of the Cult of Laughter could have their own moral code, albeit a deeply twisted and/or incomprehensible one (like some variations the Joker from DC Comics): they may commit certain horrible acts "for the lulz" but be horrified by other horrible acts simply because they aren't funny.

What do you think? What other rules of engagement might govern factions or weigh on the conscience of their soldiers and commanders?

I would say that most of the Houses wouldn't raze non-combatant villages. But that's more pragmatism, they need subjects.

Aside from Moon and Star probably. And the Earthborn would probably have few qualms about killing unicorns while Stormwing has that decree concerning "traitor" pegasi. The Everfree Tribes I expect would do the opposite and destroy villages, but they would not tolerate any sort of WMD that might harm the natural world.

I don't see the Cult having any laws, they're pretty much Chaos incarnate.

4959859 I guess the Cult has two simple rules;

1. To never leave the party until the party is over.

2. To smile and have everypony smiling.

Failure to uphold these two simple rules results in a grusome death, followed by being turned into a Smiling Doll.

Not only would the Cult give zero damns about any laws, whether they be spoken or unspoken by any house, they would probably go out of there way to break them, for the sense of defiance, and to horrify witnesses.

4959488
Well, for starters:
- Unless they have a revolt planned out, slaves showing disobedience on practically anything won't end well.
- The Church of the Celestial Sisters should have moral principles to ideally be followed by the religious. But the matter of how they are to follow it is entirely and individually under their own choice.
- Knights are warrior monks, not necessary nobility, devoted to the faith, and as such would certainly have an extra set of rules (The same goes to priests and priestesses too, I should note, for this statement, that is not the following next -->) , extremely likely to be similar to our Chivalric Code.
- And Inquisitors... they would have rules, but not the kind that binds them from performing their duties...

"Silent enim leges inter arma"
Laws are silent in time of war.
Marcus Tullius Cicero
Philosopher, Politician, Lawyer

It is best to note that a universal law of war can't really be applied to this. And if so, what dictates our beloved warlords and their subjects to follow it? Suppose that the original Equestria follows, and/or possibly made, a law of war similar to the Geneva Convention along with other powers of the world. Fast forward to Equestria Divided and see who would follow it. Only Moon and Staris quantifiable to be considered Equestria since the entity is not a separatist in any manner, while the other five are.
- Earthborn was born from rebelled Earth Ponies.
- Stormwing has its beginnings from the Royal Pegasi Guard officers who fled from the capital.
- Whitegold is a city state declared independence.
- The Tribes and the Cult are outcasts both, enough described.
Now technically, Shining and Cadance are both on the throne of Equestria. This makes the current Moon and Star technically Equestria. Are they bound by laws of war? Well... they may say on the diplomatic table that they would like to have those laws lifted so they may better Take Equestria Back...