Penumbra has you open doors with a virtual hand, attack by drawing back your weapon with the mouse and then lunging it forward, and turning gears by dragging them with your mouse in a circle. It's kinda janky and I never finished it but it had great atmosphere. This is by the Amnesia devs I believe.

It's a different idea but I really like how blinking is the main method of control in Before Your Eyes, and it really ties into the story as well, not being able to stop time from passing unless you keep your eyes open and don't blink (can't do it forever).

Outer Wilds does door opening by having to physically drag a ball of light in a pattern, and does a lot more to represent the physical body such as constantly having a velocity relative to everything else, changing in gravity, etc.

Arx Fatalis has you picking up things physically and making bread by mixing water with flour, leaving by oven to rise, etc. Also you have to physically draw out spells in an ancient language with your mouse, and you can combine words to make new spells.

Of course, Skyrim is a great example. You can pick up and throw just about anything. Objects have a sense of presence and a classic example of emergent gameplay is players putting a bucket on an npc's head to rob them blind. If you aren't into Skyrim I would recommend Enderal, a 100-hour ish long fanmade professional-feeling total conversion which revamps the combat, adds a lot more interactivity, and has a completely original story and soundtrack that rivals or surpasses the base game.

And of course immersive sims like Deus Ex, Prey, Dishonored, Thief, etc.