Dummied Out: A couple dozen ships don't spawn in vanilla Terran Conflict, though most were never actually finished and use other ships as placeholders. The Valhalla and Woden, on the other hand...
Manual Misprint: X3: Reunion's manual was wrong in almost every way. X3: Terran Conflict's manual is more accurate, but some images are wrong (Boron ships with an Argon ship for the picture) and it talks about weapons that don't normally exist in the game.
No Export for You: Some of the tie-in novels never made it out of Germany.
The Bonus Pack scripts released for each iteration of the games are the best-known, officially signed mods that won't mark your save as "modified". Also the X-Superbox also includes three fan-made soundtracks, additional signed scripts, and PDF versions of fan fiction from the forums.
The 3.0 patch for Albion Prelude is composed almost entirely of content written by the AP Community Project, a group of X modders brought in by Egosoft to get more content to tide over the playerbase while X: Rebirth battles its way out of Development Hell.
The developers of the X3 Xtended mod, who were later hired on by Egosoft for Terran Conflict. In turn, some of the guys who worked on Xtended Terran Conflict were brought in for Albion Prelude.
About half of the new ship content in Terran Conflict (Heavy M6 ships, a full ATF ship roster, frigates) originally appeared in Xtended, albeit less polished-up. Likewise, much of the new content in Albion Prelude came from Xtended Terran Conflict; the M7C Drone Frigates, Yachts, and Heavy Freighters (TS+) first appeared in the mod. The Stock Exchange is based on a script for X3: Terran Conflict, but is more fully integrated into the game and easier to use.
Technology Marches On: Real Life example for X3. During the first half of the 2000s, CPU processing power (the main limitation on the game engine) was jumping upwards rapidly, and apart from graphics the X3 engine had barely been updated since its original incarnation in X: Beyond the Frontier. If the trend of increasing processing power within a single core had continued, we'd have no problems with more player assets slowing games. Then the industry standard changed to increasing computer speed by way of multiple cores in a single CPU, cores that were often slower individually than the single cores the X3 engine worked best on. To make matters worse, the engine is 32-bit, meaning it can't take advantage of more than about 3 GB of RAM. These two factors make the restart point for an all-plots-finished Terran Conflict player not "whenever I get bored", but "whenever my installation becomes nearly unplayable".
The latter point in time even happens occasionally before the player finishes all the plots.
The change in industry trend has prompted Egosoft to build a new game engine from the ground up for X4: Foundations, one that is multicore- and 64-bit-compatible.
Trope Codifier: A major codifier for Wide-Open Sandbox space sims (particularly single-player ones), especially since Freelancer creator Chris Roberts took a ten-year vacation. His current project Star Citizen is drawing a lot of comparisons to X (and to EVE Online, since it's an MMO).
Egosoft teased an X MMO after X2. The site is still up, but nothing ever came of it (partly due to fan consensus consistently preferring single-player).
X: Rebirth was accused of this due to massive delays (it was supposed to be out Q4 2011), but Egosoft consistently denied it. It eventually came out in Q4 2013 and was critically panned, because the delays weren't enough to make it a properly playable game.
don't spawn in vanilla Terran Conflict, though most were never actually finished and use other ships as placeholders. The Valhalla and Woden, on the other hand...