If you are searching for a late game way to get reputation, here is a nice one: Warp through the space of the respective faction over and over. At some time, you will meet ships that will try to extort you. Do not block comms! Negotiate. If Captain has picked his talents properly, you will succeed in most cases. This takes a long bit, but it is an easy way to get good reputation if there are no missions available. This is confirmed for all factions.

You can unflag. There is an unflagging service on the Estate. Just teleport in and talk to the guy leaning at a cargo container next to the teleporter. You can also get unflagged by the trading bot on Cornelia Station. To find him turn left from the Teleport Pad towards the hole in the center and then drop down one level, it is a large robot in a corner. Ther also is an unflagging service at the burrow costing only 5k.
Thanks to SirKnumSkull and obvious for additional info.

Chaos level 6 stops the spread of infection. You might want to get to that as quick as possible. Easy ways to do that are:

• destroying every ship you meet (Block long range comms recommended),
  
• getting "free" repairs (by killing guards and overriding screens),
  
• getting "free" warps (by killing guards and overriding screens).

Be aware that enemies will get stronger when you max out chaos.

About Cargo inspections: They always occur when you are warping close to Sector 0 (Outpost 448). You are told to warp to a sector always close to Sector 0 which is always the same since you spawn with your ship inside of a station when exiting warp. They only occur 2 or 3 times judging by what I know. If you are carrying contraband cargo, put it in the secret cargo compartement if you have one. Else pray. If there are contraband items in your lockers (like borthix or sundust) give them to one crew member and hide him in the hidden compartment as well. For smuggling missions, I recommend Carrier or Stargazer. Don't let yourself get caught - you will be shred to pieces. If it comes to the worst - use the atomiser for the contraband personal items and chuck the cargo items into the space (untested if actually works) as Captain.

Everyone can save. You should always have the captain and one crew member save each jump as failsafe and to prevent trolling. I personally do not like anyone taking over and playing it with other guys when not having played much with me. Some guys deserve the save, though.

Be polite. It seems simple, but I have seen a lot of people insulting me or other crew members. You cannot even guess how far being polite brings you in this game. As a Captain, you should kick the rude ones for the sake of crew morale.

Get into a warp gate before it aligns. It saves you some precious seconds.

Talking about precious seconds: Respawning is a queue. This means if Person A has a respawn time of 30s and B one of 5s B would have to wait 35s for respawn if they die at the same time. Since you only die when things get interesting you might want to shorten this time. Long text made short: As Captain, make everyone get the Custom DNA talent (before the health boost).

Take your class specific talents first, because you are the only one who can and usually they are pretty good or even badly needed. Since they are usually the bottom-most talents the rule of thumb is: Start from the bottom.

Also: whenever not sure about anything concerning talents: ask. You may waste a point for doing "faster research" after having all the research already done or even 4 points on faster missile lock-on after getting the Keeper Beam installed (which does not have missile shooting capabilities).

Looking for a way to get rid of contraband stuff (i.e. borthix)? Sell it to A.O.G. traders. Especially those at the Estate buy them. (Do not sell mission items, though!)

Auxiliary reactor is awesome. Every good engineer turns off unnecessary aux systems, but the real value of the Aux Reactor is often underestimated. On my ship, with every unnecessary system turned off and the Engineer's Aux Reactor talent maxxed out, I get +9000MW!
This not only cools down the normal reactor (because it's actually not used unless you use over 9000 power), but also reduces your EM-signature.

Shock drones are very dangerous and come mostly in groups of 3. But they nearly always have an epic reactor and hull. Their Lighting turrets, shields, and sensors are pretty good also. This makes fighting them worth the effort - if you can survive. For example, lately one dropped us a Lvl 10 CCG Hull Military Grade (7000 integrity, 141 armour)! Good tactic is getting racing thrusters and RUN! Go on a distance >8km and they will not shoot you and are quite easy to kill. To get to that distance, take every effort you can (Thrust Booster program comes to mind). Be aware that they can shut down your ship and you will need to reboot it - have the Engineer ready.

Not sure if this is a bug, but I'm including it for the sake of completeness (will cross it out if it changes later on). Connected to #13.

A Weapon's listed range is the range at which enemies with that weapon will use it against you, not its actual maximum range. You can shoot the "8km range" Main Turret from further on and deal the same amount of damage.

This means that once you get further than 14km from enemies, you can just easily pick them off one by one, without taking any damage.

Headshots work. You do about twice as much damage when shooting the enemies' heads.

For the researchers: It is highly efficient to save 3 purple and 1 white research point from the beginning. You can spend them in the talent that makes you see research material on scanners. This makes the search for research much faster.