Counter-Strike
Every MOBA that exists (DotA, LoL, HoN, etc)
Team Fortress
Killing Floor
PUBG
Natural Selection
Undoubtedly, many more that I can't recall off the top of my head.
Tower defense games.
Warcraft 3, the birthplace of so many amazing genres.
>Counter-Strike, Team Fortress, Natural Selection
These games used the GoldSrc engine. Any game built on this engine gets called a mod. But this is not what most people actually think of when people are talking about mods. Rust is not a mod of Unity. These are game engines that people built a game using.
>DotA
This was a custom map. Not a mod.
>LoL, HoN
These were built on in house game engines and were not a mod.
>PUBG
This game used UE4 and was not a mod.
The autochess genre (Teamfight Tactics) is basically a mod of a mod since it started as a custom game in Dota 2.