The game creators of X-Games. The official site contains downloads, scripts and a large forum.
Xai Corporation: Research Station Alpha
This X3/X2 site covers mainly scripting; featuring pre-made scripts and a help guide on how to make your own scripts called the msci-handbook.
X3 - Database
This large website contains lots of useful information from ships, stations, maps and more. The site can be viewed in either English or German.
Apricot Mapping Service HQ
Apricot website features many scripts and mods to make X3 more 'fun'.
If you ever want to make a script or mod for X3, you will need doubleshadow's tools!
The X Universe
Home of the X3:R XTended Mod amongst others.