Glancing through my $HOME folder I see several directories
created by applications that break the common rules of prepending ".".
Among the folders that I have never created manually are "C" (wine
default),
"ccl" (freecraft), "dcc" (no idea), "music" (no idea), "evolution"
(I'm still running an old Evo, this should be solved with evo-2.0).
Plus, there are "visible" files created by (probably the same)
applications.
Also, the home folder is sometimes used to install user-specific
applications. Of course, you could collect them into a subfolder ~/bin/,
but would you want that visible on the desktop? Well, I guess you
wouldn't.