The Babylon Project is a well-known Total Conversion (standalone) mod based on the Babylon 5 universe.

Beyond the Red Line is a Total Conversion based on the Battlestar Galactica universe. Notably, it was featured in Popular Science's "How 2.0" to build a homebrew flight simulator.

Wing Commander Saga is another TC mod based on the Wing Commander universe. It features several user-made cutscenes and has released a prologue and two tech demos.

FSPort is a port of the FreeSpace 1 campaign to the FreeSpace 2/FS2Open engine. It now includes missions from the FS1 expansion pack, Silent Threat, as well as graphical improvements on the original media using FS2Open.

Inferno is one of the oldest, largest mods for FreeSpace 2. Although R1 does not fully take advantage of the SCP graphical abilities, it features a considerable number of new ships and weapons, as well as a full campaign.

Nukemod is an experimental mod by Nuke that takes advantage of several improvements of the SCP. It is still unreleased.

Diaspora is a single and multiplayer space fighter combat game set in the reimagined Battlestar Galactica universe, founded by former members of the Beyond the Red Line team.

Fate of the Galaxy is a reboot of the Star Wars Conversion mod, that has now been in development for several years. The goal is to bring a Star Wars fighter combat experience to the PC unlike any before it.