Do you use the Stallmanian version of "free" (engine open, closed assets okay) or the more stricter (engine open, assets under free license)?
If the latter: I don't know of any.
But there are a few liberated games classics that require you to have the assets from another source:
Jedi Academy:
grayj/Jedi-Academy
System Shock 2:
Interrupt/systemshock
Doom / Doom 2 can be played with Chocolate Doom and the original wads, but there are some pretty neat Doom mods and levels that are story heavy, and, given that the engine is liberated, can be seen as free software. A map that turned some heads is "myhouse.wad".
Here is also the account of id, with Doom 3 under the GPL:
https://github.com/id-Software
Most of these games are considered classics of the genre :).