Homebrew/nix: The most obvious one. MacOS just has no good package manager. It's even worse than Windows, which is also pretty bad, but at least on Windows you can install an app and manage it in a central "Add and Remove Programs" view, and they've standardized an installer format that cares about and manages versions and upgrades.

Middle Click: This is a galling one.

Rectangle: Far better than the MacOS's native snapping, which is half-assed.

AltTab: MacOS's keyboard driven app and window switching are terrible. It feels like they don't test for use that's not entirely mouse-based.

Mac Mouse Fix/LinearMouse: Real mouse support on MacOS sucks, and the unified settings between mouse and trackpad really sucks when you have to occasionally use both and don't want them to behave identically.

Karabiner: MacOS's keyboard mapping is incredibly underpowered.

AeroSpace/yabai: I don't use these anymore, because these also were pretty buggy for my use case; instead, I just use MacOS without Spaces. I hate MacOS window management, but find it less painful if I just lean heavily on tmux. MacOS Spaces are completely broken, especially on multi-monitor. They never do what you expect. I could write a screed on exactly how broken they are, but I won't in this post.

Ice (might be sketchy now; had an ownership change): Lack of menu bar overflow on MacOS is awful. I have icons that just disappear into the notch and can not be clicked, and there's not space for much, especially if you use something like Stats to see resource use.

BetterDisplay+MonitorControl: Non-retina monitor management on MacOS is bad.

SoundSource: Per-app audio control just doesn't exist otherwise.

These are all things that work fine out of the box on KDE and even Gnome. MacOS, for a very UI-focused OS, is simply terrible to use graphically if you're not baby-ducked into it from a young age. I've been using it for years at work (because my options are MacOS and Windows, and MacOS for all its flaws is still less painful than Windows), and I still can't get used to all the bad decisions. Spaces are the most shocking example of something that should work that doesn't, and they still don't fix it year after year.