Note that this tutorial is also available on the X-wiki in nicer format and you can change any mistakes you may find.
This is my attempt to make some X3 related tutorial. I tried to write it so even inexperienced users will be able to follow it.
However it is not meant to be used by everyone. Yeah and try to be tolerant to my lack of English grammar

What does "unpacking the game" mean in the first place...
Most of the data which are part of X3 game are hidden in so called catalog files. Those are the files with extensions .cat and .dat. Most of games are using this technique. The most famous example is the .pak archive developed for Quake.
So to unpack your game means to extract all the files from the catalogs into somewhere. You can extract them into some separate directory or you can extract them into the main X3 directory.
Why should I extract the catalogs?
You probably shoudn't

A little variation on what someone on this forum says in his/her signature: There are 0100 types of people - those who need to unpack the game and those who don't.
People who need to do that:
If you are/want to play with 3D modeling then you must do that. You will be able to access all the scene/body files, you will be able to import the models with DBOX2. And you will always know that the game is using the "right" file - because there will be no catalogs/mods to worry about.
People who may want to do that:
If you are playing with modifications on general level, altering the T files, you simply want to know "what is inside".
People who don't want to do that:
If you are scripter then there is no gain by having the files unpacked because all the scripts are unpacked by default (and in fact they cannot be ever packed). You will of course need to access the xml resource files but you just can extract these files and nothing more. If you are a scripter then you spend all your time on messing with the script editor (looking for the right commands


People who shouldn't ever start thinking of doing that:
If the first place you visit while on Egosoft is anything other then X2/3 Scripting and Modding. I'm serious...
So you made it here so you probably really want to know how to unleash the hell - don't you?

Before I will tell you how to do that, lets talk about where to do that.
You have 3 choices how to unpack the files:
1) Unpack them into separate directory aside from X3 game.
2) Make another copy of your game and extract the files directly into that directory
3) Unpack directly into your one and only game directory
Let's start with option 3. You shouldn't do it. There is however one exception. It is said that by unpacking the catalogs, you can gain some performance. Theoretically it should be true but I never noticed anything. But if you want to do it, you are welcome. But I would recommend to do the option 2) - much safer and you can compare the performance.
Option 2 - This means unpacking/decompressing the files and deleteing the orignal catalogs. Of course having 2 installations of the game will eat some of your free space. 1.9 GB to be precise. That's the size of the data which are not in the catalog files. The rest is in the catalogs which you would unpack anyway so you cannot count their size as lost space.
It will cost you, but it is the best option. You will have game where every file is only once, so you no longer have to worry about "which file is used now?". You can alter the files directly without need for mods - modders heaven.
Option 1 - same as point 2 but you will save the 1.9 GB as you will not have to copy the "normal" game data. Aside from that, you can also decompile all the bob files into bod's. You cannot do that with point 2 as the game cannot load large bod files.
Option 1 and 2 are for 3D modelers. You will need both of them as you will need to decompile all the bob files and you also need unpacked game so you can easily test your models/scenes without the need to make special mod catalog every time and worry about whether the files are really loaded or not.
Option 1 is for people who want to just look on the game files.
Option 3 is for people who are low on disk space but want to try to increase the game performance (although I'm not sure whether it helps)
How to make another installation of your game
That's pretty easy. All you need is to copy the game directory. No installation is required. You don't have to copy the catalog files
as you will not need them (because you will have all the data unpacked).
How to unpack the files with X3MM
For those who managed to get here but still don't have the ModManager and don't know where to get it

You may think that the process is incredibly coplicated and maybe thinking about printing it so you won't screw anything but with the X3MM it will only require few clicks.
Start the X3MM and open 01.cat
Click on Extract button. A dialog will appear. It must say Extract catalog to. If it says Exctract file xx or Exctract n file(s) then close it and click on the arrow next the to Extract button and select Extract whole catalog.
Now make sure you have Decompress files during extraction and Preserve file paths CHECKED.
Select the target directory. If you want to extract into separate directory then select that directory, else select the root directory of X3 installation where you want to exctract the files (example: D:\X3 Reunion Unpacked). Press OK.
Now open catalog 02.cat and repeat the process. When asked for file overwrite press All
Do the same with all the catalogs in the main game directory (1 to 5 for X3 version 1.2)
That's it. If you were extracting the files into second game directory and you copied all the game files, you can now delete the catalogs as they are no longer needed (and in fact they must not be present otherwise the game would use them and not your unpacked files). Be sure NOT to accidentally delete the catalogs from the original game directory!
Things you should know when running multiple game installations
Savegames are saved in your Documents directory in your profile. That means that you have the same savegames no matter what game installation do you start/play.
Mod catalogs on the other hand are in the mods directory in the corresponding game root, so you will have to copy them to all your game installations if you want to use them.
When you activate some mod in "installation 1" and then later you start game from "installation 2" and the activated mod is not present in the mods dir of the game, there will be no mods selected in the Select Mod Package window, but you must press the Original button otherwise the game will crash. That's because there is only a file name of the active mod stored in the registry and the game will try to open the file from within its own mods directory. A this will fail as there is no such file. Of course it wouldn't hurt anyone to handle the error in a different way then calling exit() (or it is abort()


If you setup X3 Editor to use your "installation 1" as data source and later you activate some mod from "installation 2" which is not also located in "installation 1", an error will occur when starting X3 Editor saying: "Cannot open mod catalog xxx". This error is not fatal and you may continue without problems.
Other things which are good to know
I will try to write these ASAP (which is considered sooner then Soon (tm)

How X2/3 is loading files - I will tell you how x3 is reading the files and how to make sure that it will use your files.