Let’s start with /Applications —
I download a diskimage of a new application and mount it, and it comes with a convenient “hey just drag me into this here alias of your Applications folder and you’re all set up!” GUIfied folder. Yeah right. Like I want all my freaking applications dumped into one undifferentiated mess. I double-click the alias to Applications and then drill down into the categorical subfolders I created there. Drag the new app into the appropriate category. The OS gets persnickety because it is set up to let you move stuff into or out of /Applications but isn’t expecting subfolders, so it makes me authenticate each time.
The next app comes as an Installer pkg file, and I click through… default location, or change? I click to indicate I want to change the install location. It lets me choose between my hard drive and, ermm, perhaps some other volume if I connect one? Accept default location, complete the install, double-click the hard drive icon and drill down into Applications, drag the stupid application file into the folder I freaking want it in, then try it to make sure that doesn’t break anything.
This notion that everything that’s an application goes into the root of /Applications would make sense if I were only going to install a couple dozen applications in total, but c’mon!
Same issue with /Documents and the plethora of applications that want to open or save or save as to this gigantic garbage midden of a folder by default. Easier to bypass, but annoying that it takes a 3rd party add-on to get these bloody programs to default to the last place I opened from or saved to.