Every game in this list has been officially released by the original developers as freeware.
There’s more I would like to add, but finding standalone downloads is tough.
Cave Story
Platform: Windows (Ported to others) | Developer: Studio Pixel | Year: 2004
Download
One Must Fall 2097
Platform: DOS | Developer: Diversions Entertainment | Year: 1994
Download
Sango Fighter 2
Platform: DOS | Developer: Panda Entertainment | Year: 1995
Download
Tyrian
Platform: DOS | Developer: Eclipse Software | Year: 1995
Download
Zero Tolerance
Platform: Genesis | Developer: Technopop | Year: 1994
Download