VSG:ResetPrefs
Many problems with VLC are due to wrong settings or a broken plugins cache. You can solve these through deleting VLC's preferences and cache.
Reset preferences from VLC
Using VLC within preferences
If you can launch VLC, in the preferences dialog, from the Tools menu, you can hit the "Reset preferences" button.
NB: This might not solve all your issues, all the time, then see the rest of this article.
Reset preferences and cache
Windows
If you installed VLC properly you can delete the preferences and cache by simply opening the shortcut you can find in your start menu:
All programs > VideoLAN > Reset VLC media player preferences and cache files
Deleting the files manually
Open the explorer and type %APPDATA% into the address bar and hit enter. This should lead you to the AppData folder of your user.
Therein you should find a folder named vlc. Delete that folder and you're done.
Mac OS X / OS X
Using the disk image script
If you still have VLC's disk image you downloaded to install it: it includes a script called "Reset Preferences", which allows you to do exactly that. Just launch it, click OK and you're done.
Manual deletion
Alternatively, reset VLC manually by removing a folder called "org.videolan.vlc" and a file named "org.videolan.vlc.plist".
Both are stored in ~/Library/Preferences - use "Go To Folder" within the Finder's "Go" menu to show this folder.
You can delete them from command line too.
GNU/Linux
Delete the ~/.config/vlc folder or execute vlc --reset-config in a terminal.
iOS
Delete the app from SpringBoard and re-download it from the App Store to fully reset the media library and settings.
