Q:

Is there a way to set the default buffer for VLC?

I'm often playing videos from my external hard disk, and, well, it has issues. It'll often spin down and it often takes 5-10 seconds to spin back up in order to keep reading files. This is really terrible for video playback, as it'll often completely hang until the drive spins back up. 
Is there a way that I can tell VLC to set a larger buffer to at least give me more buffer into the future so the drive will have time to spin up when the buffer runs out? 

A:

--file-caching seems to be what you're after.  Do you start vlc from command line?  Then you can add 
alias vlc="vlc --file-caching=10000"

to your .bashrc.
Within the GUI you'll find the option at Tools->Preferences->Show settings: "All" -> Input/Codecs, and then scrolling down.

