In The Witcher, keys are almost exclusively, but not entirely quest items. As such, they are placed in Geralt's quest item inventory pocket and they stay there, safely. They can not be lost which is very handy. There are quite a few keys in the game and many of them look alike, hopefully the list below will help make sense of them.
Key with no other label, actually the key found on the corpse of the thug who gives Geralt the A Ghost Story quest. It opens to the door to that house only.
Key to the cemetery gate, received along with the formula for Petri's Philter.
Chapter III[]
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Key to Trade Quarter sewer entrance (received from Yaevinn and/or found).
Bandit's key. The key to the fisstech lab in the sewers, two copies, one from each guard.
Key to the zeugl's lair. Found on the corpse (Gramps model) inside the Trade Quarter sewer entrance.
Keys are neither required nor found in Chapters IV and V.
Epilogue[]
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Old key to cellar door, found in trunk in first cellar (of the safe house) with Vetala.
Old key to sewers (zeugl's lair), received from a wounded knight of the Order, or Triss.
Ornamented key to the Grand Master's chambers. Taken from corpse(s) of Knights guarding the entrance.
Non-quest Item keys[]
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Key to Ramsmeat's place in the Temple Quarter slums, which you can acquire by killing his guards at night (apparently, he is not bothered by this in the least). This is the only key in the game which does not go into the quest items inventory pocket, and so, could actually be lost or accidentally dropped. Of course, depending on how you make your choices in this game, you may never need this key, and you can just pay the guards (20 ), but that is each time you want get inside.