After installing many plugins in my ~/.vim folder, I feel I no more understand the contents of that folder and I don't feel enough confidence about deleting the plugin from ~/.vim/plugin to uninstall a plugin. What if there are related files in other directories? What if the documentation was already registered (:helptags), yet the plugin will be removed? Is there any procedure to uninstall vim-plugins? I don't really want my Vim to end up being as messy as my Windows.
Answer
If you want to uninstall a plugin which was installed into ~/.vim manually, you should redownload its archive, list its content and manually remove everything, then run :helptags again (this will remove missing tags). If plugin was installed from a vimball, see documentation for :RmVimball. Vimball archives normally have .vba or .vba.gz extensions. In case you don't remember vimball file name, it is contained into ~/.vim/.VimballRecord file.
In order to avoid this problem in the future, try vim-addon-manager plugin. Like pathogen, it puts each plugin into separate directory, but is also capable of downloading, installing and updating them.