To name and shame some culprits (the one's who have shame, I won't name java because I won't expect them to care)
1) Mozilla
2) Gnome
3) Gimp
4) GPG
5) Thunderbird (Why is there a sep directory and not under .mozilla)
6) mplayer
I guess one reason why this occurs is that it's easier for to be carelessly cross-platform this way. Except you'd expect better from mozilla, specially because they store Windows stuff very well inside %localappdata%
1) Mozilla
2) Gnome
3) Gimp
4) GPG
5) Thunderbird (Why is there a sep directory and not under .mozilla)
6) mplayer
I guess one reason why this occurs is that it's easier for to be carelessly cross-platform this way. Except you'd expect better from mozilla, specially because they store Windows stuff very well inside %localappdata%