These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
gm_construct and gm_flatgrass are this for the regular sandbox mode, but they're slightly more justified in that they're the only two official maps that come with the game (not counting ones imported from other games), whereas rp_downtown is a custom map.
Base Breaker: The update that removed HLDJ and HLSS functionality. Garry got tired of micspammers and complaints about them and, in a rash decision, disabled "voice inputfromfile. Eventually, Garry saw the complaints about removing the line of code were even more annoying than the complaints he got for allowing mic spamming, and reenabled it.
GMOD 10 being less pose-friendly than GMOD 9. People got around it, however.
Game Breaker: It's almost as if there's a SWEP competition for the most powerful weapon to ever be made.
The giant "ERROR" model that replaces objects if their models can't be found. Especially if it's moving... *shudder*
Even worse, when you join a server and see a bunch of errors flying by with a player held upright in a prisoner pod made up of a pink/black checker pattern, then it turns out they just made a car of custom materials and models.
They Changed It, Now It Sucks: The menu screen was changed from a Citizen putting a traffic cone on the G-Man to a more serious shot of a Citizen holding the Physics Gun over his shoulder and the Tool Gun in the other hand. Some people were not amused. This changed in Gmod 13 as they now have various backgrounds that allow you to add or remove any backgrounds that you want.
Gmod 13 removes the turret tool and many others, they can be easily downloaded via the workshop though.
The removal of the toybox in place of the new workshop support, Garry did his best to get players used to it saying that it was not a bad thing. It isn't helped by the fact that downloading larger addons can cause not only the game itself to crash but the Steam program as well.