First time I heard it was in the original Tony Hawk Pro Skater game, every time you did a neat trick, you'd hear the same crowd cheer clip. I thought it was really annoying (I must have been ~14 yo at the time). Later as I got older, I started to recognise the same clip everywhere, with the same effect as you describe (immediately snapping you out from suspension of disbelief).
It is also used a lot in 'live' audience reactions, such as talent shows, stand up comedy, sitcoms, etc.
I also often notice sounds from Heroes of Might and Magic III in movies, probably coming from some sound bank…
When you hear a toilet being flushed in a movie, it is the exact same stock sound. It makes me realize immediately, that I just watched an actor walk in frame (sometimes fidgeting with their belt), while the effect was added later during editing.
Same thing with doors. For a long time, movies and TV shows have pretty much universally used the exact same stock sound of a door being closed. The sound effect is fairly recognizable and about as subtle as the Wilhelm Scream. Sometimes, you can even see that the door is not fully closed, but we still hear the latch snap in place. Sometimes it's also fairly obvious that this kind of door can't possibly produce that kind of sound.
I guess people working at the studios have realized that too at some point, and in the past years increasingly (but not completely) moved to a different, more subtle door sound. It's now become a bit of a "will they/won't they" moment of suspense, whenever I see a door prominently in frame for a character to walk through it.
I can notice those things, particularly when they fit the scene well, and still appreciate them as a part of cinema on one hand, but still maintain my investment in the narrative on the other.
Like when my heartstrings are being pulled. If it's done well enough, it doesn't matter if you realise in the moment that it's something the filmmakers are doing deliberately; you still feel the emotion. I can appreciate the craft at the same time as being invested in the story. I enjoy appreciating a film on multiple levels at the same time.
To be sure, Wilhelm is more of a "heh, nice" moment than a "wow, what incredible craftsmanship" realisation. And, to my knowledge, it's never used inappropriately, e.g. in a historical tragic war scene. If it showed up in, say, Saving Private Ryan or 1917, I probably would be annoyed in a way that I'm not if it showed up in an MCU or John Wick installment.