Get the E-tech talent Signature Jammer ASAP. Patrol early and often. Surrender to the cops (military officers, zealots, spies) at >-20 Rep and 0 or lower hostility. Surrender to rent-a-cops (bounty hunters) at >-20 Rep and -1 or lower hostility. Only take missions against independents or factions you're ok with being enemies with or make up the rep loss by patrolling. Don't blow-up enemy ships or ransom enemy crews and steal cargo and fuel sparingly unless your OK with making enemies or doing a lot of patrolling. Check out the 8th level pirate talent Menacing Demeanor and the 8th level diplomat talent Magnanimous Victory and consider getting them. Pay attention to trade bans and plan your trading accordingly.

Lengthy explanation below.

I find that most of my reputation lost is caused by three things: missions, ship encounters, and ship combat.

Missions

Factions don't like it when you work against them. I find that with my captains that make most of their money from missions this is where most of my rep goes. The only way to mitigate it is with the 8th level pirate talent Menacing Demeanor. If I plan on doing missions a lot I usually make it a priority to get 8 levels of pirate on an officer with a decent intimidate skill (usually my quartermaster) just for this talent. With this talent, your reputation loss for doing a missions is reduced by the pirate's intimidate skill to a minimum of -1. This can potentially cut your rep loss from missions to 1/10th or more. I've seen missions that lower my rep by as much as -19 so with a high enough intimidate skill you're only losing 1/19 as much rep per mission!

If you don't want to make getting this talent a priority I recommend choosing a few factions you're ok with hating you and taking only missions against those factions. Missions against independents don't cost rep because your rep with independents is always 0 - they aren't really a faction, they're a bunch of people who ignore faction politics - so independents are fair game.

Alternately, you can take some time to patrol after every mission to raise your rep with the faction you were just working against. If I find I just took a rep hit from doing a mission but I still have time before the mission is due I patrol the hostile world before I leave. I'll talk about that more later.

Ship Encounters

It is possible to lose a lot of rep from ship encounters if you're not careful and even with rep mitigation talents that negative rep can add up fast, so here's how you avoid it.

Rep Mitigation talents: the 1st level E-Tech talent Signature Jammer will go a long way towards keeping everyone from hating you. Its available at level 1 and mitigates rep loss by up to the character's electronics skill. In practice, this means that you'll rarely lose more than 1 rep from a ship encounter if you have this talent. I always take this with 1-2 of my starting E-techs right away.

There's also the 5th level smuggler talent Garbled Identity that does the same thing only with your smuggler's stealth skill instead of electronics but I rarely use it because its available later and smugglers usually have a lower stealth skill then E-techs have electronics skill.

Encounters with the Cops: Military Officers, Zealots, and Spies

Captains of these professions are military and nature and function as faction law enforcement. When you interact with them, you're best bet is to act like you're interacting with the cops.
In practice this means that you should watch their hostility level. If its <1 they will report you to their faction when you leave unless you surrender to let them search you. If you're not carrying illegal goods or mission cargo for a mission against their faction and you don't have <-20 rep with their faction, its best to always surrender to these unless they have a hostility of 1 or higher. You'll only see a hostility of >1 when their faction already likes you or you bribe them (or use bribe talents - more on that later).

Encounters with Rent-a-Cops: Bounty Hunters

Bounty hunters work similar to the above professions but are only interested in you if you seem like a pay day. In game terms, this means that they won't report you if they have 0 hostility but they will if they have a hostility of -1 or less. Feel free to retreat from these at 0 hostility but at -1 or less your best bet is to surrender to let them search you unless you are carrying a mission passenger against their faction or have a very low rep (in which case they will send you to prison or, with very very low rep on higher difficulties, execute you). They don't care about illegal cargo, however.

Encounters with Everyone Else

I've noticed that with low enough hostility (not sure the threshold) explorers, merchants, and smugglers will report you to their faction when you surrender to them. If you get into an encounter with one of these and retreat is not an option, consider bribing them until retreat is an option to keep them from reporting you.

You will never encounter rep loss for running from or surrendering to pirates. They will loot your cargo though so be careful.

Other Considerations: Disgrace, Arrest, Execution

With <-20 rep with a faction surrendering to a non-pirate faction ship will result in disgrace. When ending an encounter in disgrace, the opposing ship gathers evidence of your crimes and reports them to their faction. This causes serious rep loss that is not mitigated by talents. At this point getting into ship combat and fleeing will cause less rep damage if you have rep mitigation talents. Weigh whether the potential damage to your ship and crew from combat is worth taking less rep damage.

With very low rep with a faction (I'm not sure the exact amount but at least >-30) surrendering to military officers, bounty hunters, zealots, and spies will result in your captain being arrested and thrown in space jail for a while. You will lose a lot of time (years) and any missions you were doing will probably expire. With sufficiently low rep on perma-death difficulties, bounty hunters will execute you on the spot while spies, military officers, and zealots will arrest you, hold a trial, then execute you. At this point its obviously best to never surrender.

Ship Combat

Fleeing in ship combat is no more of a rep hit then retreating from a captain that wanted to search you, but winning ship combat can cause a lot of rep loss depending on what you do.

Defeating a ship by blowing up its hull will always cause rep loss that can't be mitigated. Selling the remains of the ship for salvage will cause additional small rep loss.
Looting cargo and stealing fuel cause small rep loss against most captains, no rep loss against pirates.
Ransoming crews and ships back to their faction causes moderate rep loss.
Destroying a ship after you've already won causes major rep loss, and additional rep loss when you sell the remains for salvage.

If you want to engage in ship combat regularly without making a ton of enemies, I highly recommend using the 8th level diplomat talent Magnanimous Victory. It reduces your rep loss equal to your diplomat's negotiate skill (minimum -1). You can only use it if you win without destroying their ship and you can't ransom the crew or destroy/salvage the ship and still use it, but with sufficient negotiate skill you can loot their cargo, steal their fuel, and even use Rough Interrogation (1st level zealot talent) and still only lose 1 rep for the encounter. Note that using Magnanimous Victory causes the enemy ship to leave, so use all your after-combat talents BEFORE using it.

Conflicts

You can also lose rep from ignoring trade bans. When two factions are in a trade ban, you will incur a rep penalty from one faction when you trade with the other. I'm more mercenary than merchant so I'm not as practiced in this play style but the best thing to do as far as I can tell is to pay attention to trade bans and plan your trading accordingly.

During a number of conflict types, using "acknowledge" in ship encounters with one faction's ships will give you a hit to rep with the other faction, presumably because factions don't like it when you pal around with their enemies. I haven't found this rep hit to be large enough or consistent enough to be a problem but it's worth being aware of.

Patrolling

By far the easiest and most straight-forward way to gain rep with a faction that doesn't like you. I highly recommend taking patrol talents on your crew dogs early. The 5th level military officer talent Commanding Sweep is very useful for this as well. I start patrolling a faction's planets as soon as I see my rep starting to slip and I'll often do this when completing a mission against them if I have time to spare before its due. While patrolling you can surrender and retreat from the pirates and smugglers you're "enforcing the law" against and still get the reputation bonus. Note that while patrolling will raise your rep with one faction you will usually lose a little rep from another faction while doing it. The powers-that-be don't like it when you bust their pet criminals.

Selling Intel

If you gather enough intel records you can rapidly raise your rep with a faction by selling them if you have a contact that will buy them. Note that while selling intel records will always raise your p-rep with a contact it will only raise your faction rep if that contact happens to live in a zone controlled by that faction and be a member of that faction. I find gathering intel records for the sake of raising faction rep to be less useful than patrolling but if you're trying to get access to a particular service from a contact or you happen to gather a lot of intel records while exploring, doing missions, or doing ship combat (rough interrogation and unauthorized access) its very worth considering selling them to someone who can patch up your faction rep.

E-tech and spy crew members have most of the relevant talents for gathering intel through spying. If you engage in ship combat a lot the first level zealot talent Rough Interrogation and the fifth level spy talent Unauthorized Access can generate a lot of intel records you can use for this purpose. Note that Rough Interrogation causes rep loss when you use it, but the rep loss can be completely mitigated (up to -1 for the entire encounter) by the diplomat talent Magnanimous Victory.

Pardons

I usually find these to be too expensive to be worth considering but they're worth mentioning. If you have a contact that sells pardons you can reset your rep to 0 with their faction for a (usually very high) price.

Missions

Doing missions for a faction will increase your rep with that faction. I find raising rep this way to be relatively slow compared to the methods above and I usually only do this when I already have a decent rep with a faction and I want them to give me better-paying missions or I want access to a service provided by a contact that doesn't buy intel. Missions are overall better for making money than rep in my experience.

Ship Encounters: Acknowledge

If the opposing ship has a high enough hostility (>1 I think) you get the option to end the encounter by acknowledging. In lore terms this means you talk to them about the weather and ask them how their kids are doing, etc. Usually this is only an option if their faction already likes you but if they don't you can get this option by repeatedly bribing them or using certain talents. You gain a small rep bonus (0-4ish) from doing this. If you do it a lot, it will add up.

The talents Faked Signature (Pirate or Spy 8/Smuggler 5) and Forged Signature (Smuggler 5) essentially work as a free bribe that you can use even against more hostile (lower hostility) bounty hunter and military officer captains. If you have more than one crew member with one of these talents you can use it multiple times per encounter. At one point I had 5 copies of Faked Signature from crew members and I was able to acknowledge against certain story bounty hunters that are scripted to have max hostility, and my rep with their faction was -80 or so. Not something that's doable early on but mid/late game its a great way to keep factions on your good side and avoid otherwise certain combat.

Mediship

I don't have much experience doing this as I'm a mercenary, not a doctor, but I've seen the strategy floating around the forums so I thought I'd mention it.

The 8th level doctor talent Generous Service can be used to create a reputation engine. What you need:
* at least one officer or crew member with a high doctor skill and the 8th level doctor talent Generous In Service. More if you land more often than once every 9 weeks of game time.
* lots of medical bays on your ship. shoot for a total medical rating of 20 or more.
* few or no other talents on your crew that trigger on landing in an urban zone. (only one talent can trigger at a time so if you have a doctor with Generous in Service and an E-tech with Listening Post there's only a 50% chance that Generous in Service will trigger when you land as the game chooses the talent to trigger randomly).

With this setup generous in service should nearly always trigger when you land in an urban zone, giving you a solid reputation bonus with the local faction just for landing. Works well with gameplay styles that travel to a lot of different urban zones (trading, certain types of missions, etc.) . The draw back is you will have little space on your ship for weapons and defensive upgrades and you'll want to avoid taking other useful talents that trigger on landing like Listening Post and Secrets Unbound.


Anyhow, I hope you found this guide helpful. Rep management can be a lot of work but its very worth it, if only to have a place to refuel. Using these strategies I was able to get positive rep in every faction late-game on hard mode while executing death warrants constantly.