I recall the INI files of Red Alert were an open book for modding the game mechanics. I had spies with silenced pistols and "tesla cufflinks". It was really fun making crates spawn super frequently. I also vaguely recall making one of the planes into a nuke carpet bombers (fun, but the forced delay each time a nuke went off was a tad annoying).
Then there were the Duke Nukem 3D CON files...