I want my space to be mine. Keep your app's stuff out of there!
Your homedir equivalent on windows (since Windws XP) is /Documents and Settings/username, or the modern shortened equivalent. That has subdirectories for documents and application settings. Apps that put config data in My Documents are using behaviour dating back to Windows 95.
It's the same on Mac OS - /Users/username has a Documents subdirectory. Mac spps tend to be better-behaved, but a few manage to pollute the Documents directory. On Linux you may roll your own or use a ~/Documents directory created by your desktop environment. The fact is your homedir is the home of pretty much anything that is user-specific, and you either need to collect all the config data into some sort of config directory, or do your own organising in a subdirectory, or both.
"My Documents" is a nightmare... I think only one folder (out of nearly a dozen) and only one file are actually of my making.
The canonical example is the backup. There's a strong case to be made for "tar czf /tmp/backup.tgz ~". Do you really want your backups to become as complicated as they are on OSX and Windows?
Likewise, being able to mount home-directories from remote servers, and being able to easily delete/move/quota users are highly desirable features in multi-user systems.