Feel free to mod these, they're simple enough they both could be altered to match whatever one feels works, and were literally brainstormed over a single night.
If you want a basic reputation system of some sort, have two compatible reputation systems.
There are two stats here, Renown and Morality.
Renown starts at 20, and the more famous you become, the higher this stat gets, and the more your story is told.
Morality is which groups cheer for you, and how your story is told. Morality starts at 50, and Morality gets higher the more you support the forces of order. Use Morality-50 to determine a given Order NPC's opinion of you. The tens digit may be used to determine the appropriate bonus (or penalty).
The more you support disorder or even just give into greed the more the negatives start to pile on and the more favorable the underworld will regard you up to a certain point. After reaching about 30 they will start to disregard your ways as too much or too unprofitable, forcing one to look deeper in the darkness for allies. Above 30 the true forces of chaos will still see you as imperial scum, but below it they'll start to become more favorable, starting one on the slow path to hell. For forces of chaos, use 30-Morality to determine their disposition towards you, similarly to the above.
This system works best for the legendary status of a Rogue Trader, but can be easily used if one wants a basic way to track morality with which to evaluate how to have various NPCs treat the players. If the restrictions imposed by the effects of Morality seem too much, the GM may waive some of them in the interests of having fun, or may instead allow the players to try and use their reputation subtly.
Organization by Organization:
Here one again has a value from 0-100 to represent how much a particular organization trusts or distrusts you. A value of 30 is the standard, and all organizations should be assumed to be at this value unless prior actions and events have shown otherwise. While all of the values are collectively referred to as Reputation, it is very much like a skill group or talent group in that there are many 'groups' you can have Reputation with--the groups one can take Peer for are good for starters, although it need not be limited to those groups! One does not need to record any groups whose Reputation is at the default 30, and most groups may be assumed to be at this value!
The higher a group's reputation value, the more the group feels highly of you, and vice versa. Reputation (Group)-30 can be used to determine their starting disposition towards you, which should be rounded to the nearest 10. The normal reputation range is thus 0-60, and most groups should remain within these values. While the explorers may raise and lower these values based on their deeds and misdeeds, the highest and lowest values require a concerted effort from the Explorers to obtain, and thus further increases/decreases should either be smaller or require notably more effort to obtain. These modifiers work very similarly to the ones in the expanded social conflict rules in Into the Storm, may be used to determine starting Disposition, and may stack with the appropriate modifiers from the system above.
Peer, Good Reputation, Enemy, and Rival add half their modifiers to the appropriate Reputation value.
While negative reputation values can exist, they should normally be specifically saved for those groups the explorers specifically make a point of pissing off and annoying, or for groups innately hostile to outsiders. A group with any negative reputation value is inclined to attack the explorers on sight--with this getting more severe as the values drop! At -30, the group regularly seeks out and tries to hinder the explorer's progress much like the enemies of a Noble Born (and indeed the same rules and mindset can be used here). The GM should be advised not to let this value drop below -30, as that is already at the point of a high vendetta, and while not impossible, it's near impossible to garner more hatred towards such a despised foe.
Due to their general hatred of everyone else, Rak'Gol and Tyranids start at a -10 for Reputation, of which raising is near impossible save under extraordinary circumstances, and for which raising one's Reputation is bound to lower the disposition of nearly everyone else as suspicion is cast upon the explorers.
In a similar vein, reputation values equal to or higher than 60 should be saved for those groups who have gone out of their way to please, aid, and advance the goals of a specific group. Those who have earned such respect will find themselves often receiving willing aid from the group who they hold such an esteemed reputation with, and higher values increase the nature of such aid. At 70, it mostly consists of very small favors, but as the values get higher, the group will willingly provide more and more aid, up to what they can reasonably provide. If a Rogue Trader and his subordinates manages to get up to a reputation of 90 or higher with such a group, they should be willing to aid the Explorers in ways that would be considered outright impossible if they did not have such esteemed reputation, although Fellowship and/or Profit Factor tests may be required as normal for the most extreme benefits.
The GM should definitely let the players benefit from such a relationship, but like any group, they reserve the right to reject the requests of the Explorers, although such is their status that such rejections are bound to be handled significantly more favorably and helpfully (with some form of explanation as to why they can't) than if the Explorers demanded something similar from an organization they only have 30 reputation with. If the GM feels the players are trying to mooch off their allies, the GM should set a limit through such rejections, and if players insist on attempting to gain something that feels far beyond their reach, the GM may either tell the players they essentially need to raise their reputation more first, as although they are highly respected, their sensibilities mean that they are still not willing to risk their position/renown/lives/etc. for such; or he may offer some quest or endeavor to be completed before it happens, as per trading favors. Continued insistence may result in a hit to their reputation, as such things leave a sour taste in both sides mouths.
Perhaps among the most significant rewards of this, and one that should be emphasized to some degree, is the myriad of unique experiences such reputation unlocks. Grand tales may be shared around the table and grand feasts may be held with nearly any organization out there, and this naturally increases as Reputation with that group increases. The Ecclesiarchy may be more than willing to take one's preferences into account when converting a planet to the Imperial Creed, or at the highest levels of reputation, specifically endorse a specific variant of the Imperial Creed. The Adeptus Mechanicus would willingly provide implants to their most favored allies, perhaps even offering Best Craftsmanship implants at a regularity most only see with Common Craftsmanship, and at the highest levels may even induct and train the more technically-minded explorers in the ways of the Omnissiah. A chapter of Space Marines may very well send a few battle brothers to accompany the Rogue Trader, battle brothers that are no doubt either happy or proud to be serving alongside them, and at the highest levels the Battle Brothers could be convinced to start a Successor Chapter in the Trader's honor. And it is very possible to find similarly unique experiences both on the other side of the Imperium, and with the many Xenos races that inhabit the Expanse.
Events like the above lead to the kind of epic tales many players would love to participate in, and as part of the motivating factor to raise one's reputation so high despite the difficulties, such amazing rewards should be provided to the Explorers from their organization--and the GM is advised to exercise creativity in doing so! However the GM should limit the number of groups that the Explorers have such an astounding reputation with to one, maybe two, and they should only be able to raise one group's reputation as high as 90 (although for the one group only, this may go above 100).
What They're Known For:
In addition to the direct benefits of having Reputation (Group) higher than 60, or the direct drawbacks of having Reputation (Group) lower than 0, reaching such glorified heights or despised lows influences not only the group itself, but those related to it. When the Explorers encounter a group with some form of 'friendly' relations with the group they have a Reputation higher than 60 with, the GM may give the Explorers a situational bonus, due to having enough fame with one group to be viewed favorably by another. This bonus should not exceed every ten points of Reputation Bonus they have above 60, rounded up to the nearest 10. Similarly, if the group has 'friendly' relations with another that the Explorers have earned the ire of, the GM may assign a situational penalty to interactions with them in a similar fashion. Finally, while the benefits of having such erstwhile allies are many, having earned their approval often earns the hate of those who oppose them, and the GM may thus impose a similar penalty for interacting with the groups which hate the Explorer's greatest allies.
One last thing to keep in mind is that having a reputation of 0 or higher with an innately hostile group casts suspicion upon the explorers to all groups except such innately hostile groups. If the Explorers somehow manage to get a Reputation of 0 or higher with those groups, and especially if they have a reputation of 30 or higher, the GM may impose a penalty to interactions with other groups similarly to the above, despite their reputation neither being as high or as low as required for normal. Innately hostile groups begin at -10 Reputation.
Where to Use This:
This system tends to fit better in Black Crusade towards the various warring factions, or towards the inquisitorial factions in Dark Heresy, but the underlying concepts and measurement systems behind them are easy enough to apply and maintain for any game. For GMs that wish to reward their players for interacting with other groups, this system provides a mechanical way of representing how well other groups and organizations see the Rogue Trader and his subordinates (or some other group of Player Characters) and gives the GM the opportunity to reward his players with something other than Profit Factor, Experience, Fate Points, or Gear.