Zelda games are also known for having these. In OOT and Majora's Mask, if you find one of those bobble head cow dolls that you somtimes see in stores and hit them with the sword or anything, they actualy move despite being part of the scenery.
Radiata Stories for the PS2 also had a fair bit of these. Your character could kick things, and you could interact with several bits of the scenery through this. Not only this, but practically EVERY NPC IN THE GAME had alternate lines they would say if you kicked them once or several times. I might pick up an emulator just to play that game again, it was pretty great with the details, battle system and the huge number of recruitable characters.
Not sure if this counts as a small detail, but in Legacy of Kain: Soul Reaver, to fight Dumah, you had to remove the spears that were impaling his body and keeping him from comming back to life. Thing is, if you shift into the spectral realm, you can see Dumah's soul hanging around his body, and even get attacked by him. Also, in the first Metal Gear Solid game, once you got the camera, you could go around and take pictures of certain places, and see ghosts in them. Most were just faded out and low constrast pictures of the developers, but some were genuinely scary.