#manually
sudo vi /usr/share/applications/mimeinfo.cache
sudo vi /usr/share/applications/defaults.list
vi ~/.local/share/applications/mimeinfo.cache

#or via sed:
sudo sed -i 's#video/webm=#video/webm=vlc.desktop;#' /usr/share/applications/defaults.list
sudo sed -i 's#video/webm=#video/webm=vlc.desktop;#' /usr/share/applications/meminfo.cache
sudo sed -i 's#audio/webm=#audio/webm=vlc.desktop;#' /usr/share/applications/meminfo.cache
sed -i 's#video/webm=#video/webm=vlc.desktop;#' ~/.local/share/applications/meminfo.cache
sed -i 's#audio/webm=#audio/webm=vlc.desktop;#' ~/.local/share/applications/meminfo.cache