During the quest "The Tower Outta Nowheres", Geralt encounters a wizard trapped behind a magical door inside a tower. The wizard claims he was trapped there by the tower's Defensive Regulatory Magicon (DRM), which locks down the tower if anyone but the original owner tries to enter it. The tower's previous owner wrote a treatise on how to remove the defenses called "Gottfried's Omni-opening Grimoire" (GOG).

The initials "DRM" are a reference to Digital Rights Management, which is used by game publishers and platforms to prevent a game's original purchaser from freely sharing digital copies of it over the internet. The initials "GOG" are a nod to the website Good Old Games, which was founded in 2008 by The Witcher 3's publisher CD Projekt. It's famous for selling DRM-free copies of games and other software so that users may freely backup and share what they purchase.

Later on, while Geralt and the wizard are escaping, the defense system notes "disturbing indications of freedom". This is likely a jab by the game's developers at aggressive DRM policies, and echoes a common criticism that DRM restricts end users from freely controlling the software they purchase.
Shortly after the game's launch, one player discovered an easy way to earn money early in the game. They could kill cows, sell the hides, meditate to replenish the herd and repeat as desired. When CD Projekt Red found out about this, they decided to stop players from exploiting the method with the "Bovine Defense Force Initiative" patch. If Geralt kills too many cows too quickly, a powerful monster would then appear which can easily kill low-level players.
Contributed by raidramon0
After completing the side quest "Contract: Monster in the Cemetery", back at the cemetery near Lindenvale, you'll come across two angel statues that weren't previously there. If you turn your back from them and turn back, you'll notice that they've moved. This is a reference to the Weeping Angels from the television series Doctor Who.
Contributed by KnowledgeBase
There is a village called "Lurtch" located in central Velen. The description text mentions it being the former location of the "Evves" family estate, the name of the former lords wife was "Mortilanca" and the name of the former family butler (and inspiration for the villages' name) was "Lurtch".

This seems to be an obscure reference to The Addams Family, particularly Morticia Addams and their butler, Lurch.
Contributed by DarkChojin
There is a chance that a human enemy will say "Your mother was a hamster and your father smelt like elderberries", this is a reference to a scene in Monty Python and the Holy Grail.
Contributed by generalcodeblue