Since you probably don't want to read that spoiler box (I know I didn't) I'll give you the vague answer.
Imperial Agent: the ending of your story is definitely different if you go LS vs. DS, though of course with no ramifications to your character/titles/etc. Of course when they add new story, a LS agent and a DS agent could legitimately go very different paths.
I've heard something similar for the Bounty Hunter.
Trooper: Not a damn difference, as I recall.
IA endings are not determined by your LS/DS. There is one ending variant which requires a specific LS choice to have been made earlier in the storyline, but you can still get it even if you are Dark V when you go to the ending sequence if you make the corresponding choice.