Some of the old single player mods for Doom 3 have never been updated to the final 1.3.1 release. This is usually because the mod team has disbanded, lost the source code or just can't be bothered. You can now play your old 1.3 mods on 1.3.1 using the new mod-helper mod "Run 1.3 on 1.3.1" :)
Simply download this file and extract the two PK4 files into the folder containing the 1.3 mod you wish to run and you're set!
This mod-helper is for the Windows version of Doom 3 only and is intended for single-player mods only. Multi-player mods may work but I do not expect this feature to work well with Doom 3's auto download system; so be warned. You will also be limited to only having Windows players joining a Windows server.
These are the "old" mods that have been confirmed as working using "Run 1.3 on 1.3.1"