- Worms: required a CLI tool to convert SFX
- Doom: WAD files were pkzip format
- Duke3D: came with its own level editor
- Jazz Jack Rabbit 2: also came with its own level editor
- Grand Theft Auto: massive modding community for the original game on PC via unofficial 3rd party hacks
- Minecraft, Roblox, Mario Maker, etc: all have massive communities of user generated content and none of that has been created via notepad.exe.
It would be harder to come up with examples, either modern or retro, where plain text files were the preferred method for modding.