One of the really nice things about MoO3 is that many parts of it can be modded (short for 'modified') to fit your prefered playing style. This guide won't focus so much on what can be modded so much as how to do it.
Note: This guide will assume a Windows version of MoO3. The instructions are similar for the Mac version, but directories and program names would vary.
The first thing to do is find the right directory. By default, MoO3 gets installed to:
C:\Program Files\Infogrames Interactive\Master of Orion 3\
From here, we first go to the GameDataSets directory, then Classic_01, then GameData, and finally Common.
In this directory you will find four files, each with a '.mob' extension. The extension is actually a bit of a trick, the files really are '.zip' files. These files can be opened with such programs as WinZip, WinRar, etc. The file we are most interested in right now is Spreadsheets.mob. If you double-click on the file, Windows will most likely ask you how to open the file, because it doesn't know. Tell it to use whichever of the programs you have installed (and if you don't have one installed, you'll need to download one before you can proceed). Once it is open, you will see it contains a single folder, aptly called 'Spreadsheets'. Click on that folder and drag it into the same directory that contains the Spreadsheets.mob file. This will copy the folder, and all its contents into that directory. Finally, you'll need to right-click on the Spreadsheets folder that was created. A menu will pop up, and 'Properties' should be the option on the bottom. Select that. A new window will open up, listing the details of the folder. What you want to find is an option that says 'Read-only', with a checkbox beside it. Uncheck the box so that you will be able to modify the spreadsheets.
Ok, the hard part is now done. You can move into the Spreadsheets directory, where you will find a large amount of '.txt' files. These are the spreadsheets themselves. They are best edited with Excel, but you can use a normal text editor if you are careful. The spreadsheets use what's called a 'tab-delimited' format, which means that 'tab' is used to separate the columns from each other.
At this point, you may begin to look at the various spreadsheets. Some important ones you'll likely want to have a look at:
TechTables.txt - This spreadsheet contains the full list of technologies that are present in the game, as well as the numbers used in the formula that determines how many RPs are needed to research each TL.
RaceModifiers.txt - This spreadsheet contains details on all of the races present in the game, as well as the various race pick options.
TaskForceRules.txt - Here you'll find the rules that determine how a TF is made up. It also lets you increase (or decrease) the size of any TF.
WeaponsTable.txt - Each of these tables contains the corresponding weapon information based on their type. It's where you'd look to make changes to any type of weapon.
Note: Do NOT edit the files inside the .mob file directly. Do not move any files back into the .mob file. And absolutely do not delete the .mob file itself.