The assets are relatively easy to get -- Steam has both games. You could either pay $9.99 for each of the games, or buy the Jedi Knight Collection, which includes Jedi Academy and Outcast, plus the Dark Forces games as well as Jedi Knight: Mysteries of the Sith for $19.99.
Separate data and engine packages, engine package distributed by Debian, data left as the responsibility of the user. That way the iD games are in debian too.
It could be packaged, without assets, but with an "installer" that prompts for a cd/source to copy from (along the lines of what ttf-mscorefonts-installer does, for instance -- or freecraft[1] for a more similar example: "FreeCraft needs a lot of data (maps and artwork), that can come from WarCraft II CD, or from the FreeCraft Media Project, codename fcmp, that has support for almost all the data present in WarCraft II. (...) WarCraft II is a registered trademark of Blizzard Entertainment.").
Off the top of my head, I know Heretic and Doom have custom models and textures from the Doomsday guys, I know there is a high res quake texture pack, there is a high res Jedi Knight pack, but none of those include levels / models / sound / etc, so they are all addons to the base games.
Freedoom is the only total conversion of a FOSS'd major game engine with FOSS assets that is actually playable that I know of. If anyone knows another, let me know, I'd love to play them.
