One day, people from the VIA association (VIA is a students’ network association with many clubs … amongst those is VideoLAN.) came back drunk with a cone.
They then began a cone collection (which is now quite impressive I must say).
Some time later, the VideoLAN project began and they decided to use the cone as their logo.
Source: http://www.nanocrew.net/2005/06/23/vlc-cone/