As the title says, I'm looking for situations in the war against the sepratists where I can put Knight level or higher Jedi in a situation (without their being able to control the setup) where doing the "Right", moral thing is most definately not the "smart", war winning move.

One example that I've worked up already- a freighter is sending an SOS, being pursued by sepratist forces intent on destroying it. They have orders to not intervene. (either "reach planet X undetected" or "Dont scare them off, the Fleet is plotting a microjump to intercept as we speak", depending on if it's in enemy or friendly territory) Do they take a conflict hit, make their lives significantly more difficult, or try and convince me they have a third option?

Are you looking for situations that will challenge the characters or situations where you intend to give them conflict no matter what they do because they have to choose between two evils? If the latter then no thanks.

Situations where they have to choose between a massive challange/potential nonfatal mission failure or conflict.

I want to push the choice of "winning" vs "doing what's right." Either option pushed the metastory along.

Morality should be a vehicle for telling good stories that engage a player with choice, this is good. Perhaps the player is scouting down some information on a murder and encounters a child who has lost its mother. Do they stop and engage the mother and risk the murderer committing another terrible act or do they help the child and return to their mission as soon as possible? To me this creates an engaging choice, and the player is free to chose the out come he wants. As the GM you would allow the player the choice and guide them to what you would consider the good or the bad of choice they are making. As you narrate the action you would give them direction, "OK you want to help the child, that is in line with your compassion morality chose so you will get double the dice roll for your morality at the end of the session, form up your perception pool and see if you can spot the mother...."

If you put the characters is a catch 22 situation where they will trigger nothing but the dark side of their morality and take the choice away from them, then you are not making a good narrative or story for the players. You are misusing a game mechanic to make the story far less interesting and removing the player choice from the game. If you have the players murder Jim because by killing Jim they can save Jack, you aren't giving them a good choice at all, and as such this isn't a situation I would apply the morality mechanic, as clearly there is none being applied.

You are just hitting the player with two amoral choices, I think for this rule to work the GM has to give a moral/amoral choice and allow the player to role play through the choices.

A "Paladin Screwjob" is the GM breaking the rule of Wheaton.

Situations where they have to choose between a massive challange/potential nonfatal mission failure or conflict.

I want to push the choice of "winning" vs "doing what's right." Either option pushed the metastory along.

Winning vs. doing what's right is one thing, but Failure or you get Conflict is a Richard GM move. I want to fall to the Darkside because I was a jerk, not because I was put in a position where I didn't really have any other options.

You don't want the Paladin screw job...

You want the Palapatine Screw Job!

Don't give the player an option between success with conflict or failure, give them the option of what they want vs. what they need.

Example:

@ Ghostofman - Totally stealing the idea, and I'm going to keep General Buttsavage as my NPCs name in honor of you!

It'll of course be pronounced "boot sav vahj" though ....

That is the sort of idea I'm looking for, but it takes a while to bear fruit. That's two ideas, any more?

The characters need to infiltrate a Separatist base of some kind. The various passcodes/callsigns or other security measures change quite frequently, at least every 24 hours or maybe less. A few hours before one of those changes a reconnaissance team brings back a Separatist prisoner with knowledge of the current codes. Unfortunately the Sep is a tough cookie and won't spill the codes just because the players ask.

Now, the players can either force the codes from the prisoner - through use of "enhanced interrogation" or by using the Force to yank the information directly from his mind - or accept the fact that they'll have to do the mission without the codes, meaning some very, very tricky Deception and Skulduggery checks, and a near guarantee of heavy combat. The quick and easy solution here should be very tempting, and you could even have some Clone Troopers volunteer to beat the intel out of the prisoner if the players display reluctance, giving them a chance to keep their hands (technically) clean while still reaping the benefits.

The episode in Clone Wars where Ashoka has her lightsaber stolen comes to mind. There are a few instances of Morality being used therein.

There was something the the New Jedi Order series (ducks to avoid shoe) where the Yuuzhan Vong used a refugee ship as a shield to further their plot, or something like that. I cant remember the complete story.

That is the sort of idea I'm looking for, but it takes a while to bear fruit. That's two ideas, any more?

Tell us more about your players and characters. What are their dreams, their desires, their most intimate of intimates?

This would be a play by post game, and so should be relatively fast paced (to make up for the slowness of play by post gaming).

On the flipside, I dont actually have players assembled yet- I'm looking to put together a stable of potential dilemas before I put up a "players wanted"

This would be a play by post game, and so should be relatively fast paced (to make up for the slowness of play by post gaming).

On the flipside, I dont actually have players assembled yet- I'm looking to put together a stable of potential dilemas before I put up a "players wanted"

Thanks for the warning! I’ll make sure not to apply for any game where you are the GM.

The characters need to infiltrate a Separatist base of some kind. The various passcodes/callsigns or other security measures change quite frequently, at least every 24 hours or maybe less. A few hours before one of those changes a reconnaissance team brings back a Separatist prisoner with knowledge of the current codes. Unfortunately the Sep is a tough cookie and won't spill the codes just because the players ask.

Now, the players can either force the codes from the prisoner - through use of "enhanced interrogation" or by using the Force to yank the information directly from his mind - or accept the fact that they'll have to do the mission without the codes, meaning some very, very tricky Deception and Skulduggery checks, and a near guarantee of heavy combat. The quick and easy solution here should be very tempting, and you could even have some Clone Troopers volunteer to beat the intel out of the prisoner if the players display reluctance, giving them a chance to keep their hands (technically) clean while still reaping the benefits.

This example echoes the thoughts I had as I was reading this. The choice the GM should set up, in my opinion (if he was set on putting this sort of choice in front of the players, I'm not entirely a fan of the idea in the first place), is between the "quick and easy, but morally wrong" and the "morally right, but makes things complicated" options.

The players shouldn't be forced into taking Conflict to complete the mission, but rather taking Conflict to reduce the difficulty of the mission. It puts the Dark Side into that "seductive" position that the universe describes it as taking.