Games of such kind I know so far:
- Warzone 2100 by Pumpkin Studios (Sci-fi, Post-Apocalyptic, Custom unit, free, open-source, GPL)
- MegaGlest by MegaGlest Team (Fantasy, Ancient Civilization, Custom faction, free, open-source, GPL, moddable)
- The Battle for Wesnoth by The Battle for Wesnoth Project, David White (Fantasy, Custom scenario, unit, and faction, free, open-source)
- Zero-K by Zero-K Team (Powered by Spring RTS, free, open-source, GPL, moddable)
- Cosmoteer by Walternate Realities, @Walt (Space, Roleplay on forum, currently free, moddable)
- Uncrewed by Quite Different Mechanics (Modern, Custom unit)
- Forged Battalion by Petroglyph Games (Modern, Custom faction and unit)
- Warcraft 3 by Blizzard Entertaiment (Fantasy, Use scenario and model editor)
- Empire Earth by Sierra Studio (All ages, Custom faction (civilization), and scenario)
- Galactic Civilizations III by Stardock Games (Sci-fi, Space, Custom faction, and unit)
- Spore by Maxis (Spec-fi, Tribal-Space, Custom unit)
- LittleWarGame (Medieval, Custom unit and scenario, free, play on browser)