The Camera/Invention System in Dark Cloud 2. Literally take pictures of things around you and use that as inspiration for inventions. It was a lot of fun.
The Insight system in Bloodborne. As you gain more insight, you see more of the true nature of the world around you and slowly devolve into beasthood/madness. Very Lovecraftian. Made for some shocking discoveries on the first playthrough.
Saving townspeople by defeating monster lairs in Soul Blazer. A great way to make the combat and fighting mean something, you can unlock the townspeople and try to save them all.
Mario 64. Collecting stars. Nothing needs to be said, it basically invented the collect-athon platformer and my OCD thanks it mightily.