In The Witcher, keys are almost exclusively, but not entirely przedmioty fabularne. As such, they are placed in Geralt's Kieszeń na przedmioty fabularne and they stay there, safely. They cannot 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.
Klawisze nie są ani konieczne, ani w Akty Czwarty i Piąty
Stary klucz do piwnicy
Zaśniedziały klucz – Klucz do zeugla
Zdobiony klucz do komnat Wielkiego Mistrza
Key to Baranina's place in the Klasztorna slums, which you can acquire by killing his guards at night (apparently, he isn't bothered by this in the least). This is the only key in the game which does not go into the Kieszeń na przedmioty fabularne, 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, but that's each time you go.