For WA i'd say Wormkit/Rubberworm, Project X requires too much faffing around so I never got into it, perhaps if it was easier to install and run, there's a chance i'd change my mind, but Wormkit and Rubberworm give me everything i've ever wanted, bar real time worms.
Arma 2- DayZ.
DayZ - Unlimited Stamina.
Quake 3 Arena - Urban Terror.
Cities: Skylines - Traffic Mod.
Fallout 4 - More building. (There's a limit on how many things you can build, this mod takes away that limit.)
Rocket League - Bakkes Mod. (Rocket League sucks now because Epic, as usual, ruin everything.)
Struggling to think of other games i've played with Mods.