Is the game focused on courtly intrigue? Is it based on defending the empire from hostile outside forces? Is it based on ferreting out heretics and dishonourable swine within the empire?
Each of these has a very different twist on the concept of honour. Noble Houses are the main political unit in the Empire. However, like in L5R, some Houses focus their attention on one another, and some focus it on the outside world; i.e. for some, it's about military defense, for others, it's about scoring brownie points with the Emperor, and for a few, it's about watching out for foreign influence and saboteurs. The mechanic that unites all of these things is the end-of-session vote: the players all vote on each PC to see if that character performed some noteworthy service for the Empire (since Honor can decrease during play, set aside any scandals or black marks on the character's record). If the players agree that some service was performed, the character gains one Honor die. *Any* service to the Empire will do. However, given that, outside the Empire and in other no-Honor areas, Honor dice do nothing, I think I might need to ramp up the importance of House influence - characters who are clearly doing good work for their House (and the Empire) will be noticed by their House patriarchs (and the leaders of other, friendly Houses). This keeps guardians and inquisitors from losing out quite so much, I think. A similar every-session vote, for service to a House and commensurate gain of House favor, would grant House influence dice that are added to any pool involving that particular House.

First glances would indicate that a game of courtly intrigue would have honour play the strongest role, but there are certainly dishonourable courtiers throughout history (it's usually just that their shady dealing aren't revealed until they die).
That's the thing - it's very important to keep your shady dealings secret, lest their reputations be ruined. And keep in mind that, since Honor is a mystical force in the universe (in the setting), but it's gained and lost through the consensus of the Imperial Court, it doesn't matter if someone really is a complete bastard, and I think it's good to have a good tug-of-war between your own glory and actually accomplishing something for your House and your Emperor.

Those defending the empire from outside forces might seem to have the least concern for honour, but even these individuals need to consider how much honour they are willing to sacrifice in order to stay true to their ideals. Is it better to ally with a lesser enemy to build a temporary alliance against a stronger threat? Is it better to keep all enemy's of the empire at an arms length to avoid the corruption they might bring? If power comes from honour, then you might also consider the notion that other forms of power come from different societal structures...
First, I agree with all of these sentiments! Exactly - these are the kinds of choices that players will have to make. Secondly, I am totally on board with the notion of "other forms of power" - other cultures definitely have different primary ideals, such as Glory, Obedience, or Ruthlessness. Whether or not they get explored, however, is a different story. It'd be up to the game group (I think) to decide whether the foreign barbarians have their own central virtue that a long-term border guard could pick up (through proving himself in battle and diplomacy, perhaps), or whether the exact same mechanical feature is, instead, defined like House influence, wherein the House in question is simply the enemy army or region of enemy territory.

Those working as Inquisitors within the empire, seeking out the dishonourable and punishing the unjust would probably benefit best from a hard and fast honour distinction.
Honor is, plain and simple, the opinion of the Imperial Court about how valuable you are to the Empire. Granted, what *they* might base it on is mighty subjective, but that's the definition of it right there.

Even if you've only got a specific "official" setting in mind, consider the possible play options for the game. Consider where people might be interested in taking the game, and how the rules can be adapted to reflect different styles of play.
Absolutely, I'll have to think about this. Games that focus a great deal on the Hairy Barbarians and defending the realm will definitely ramp up the tension between a respectable objective (defending the realm) and making concessions for the Court's input and their concept of respectability.

What if a player whose character is Aloof wants to participate in those politics? How would that player's character choice become meaningful?
An Aloof player simply has less at stake engaging in House and courtly politics, but is absolutely welcome to engage in them. However, this draws in the danger of irritated noblemen trying to get the monk ejected from his Order for speaking his mind too freely. I'm not sure how one loses the Sorcerer status, but they, like Dishonorable characters, can still partake of the Houses' jockeying for position; they would focus more on working on behalf of their preferred noble Houses, however, instead of being called upon to appear in Court.

Yes, but it seems to me that there should be "Honor-only" areas, if only to make me think twice about choosing an Aloof character. (I know I am starting to repeat mysef...)
Ooh, Honor-only areas are good! In Court, particularly if a monk has some kind of nobleman ally with him, he could function normally (canceling out Honor), but other than that, and certainly in the depths of a powerful noble House, an Aloof character would definitely be at the mercy of Honorable characters.