Working around Youtube Content ID system

Audio
If your clip contains licensed audio (mostly songs) you can do 2 things:
Silence the licensed part using audio editor
Speed increase of 5% or greater, using audio editor
Increase the audio pitch by 5%
Read this article for more info: http://www.csh.rit.edu/~parallax/

Video
If your video is identified as licensed content there are still options you can do, which require you to use video editor.

Change aspect ratio to 16:9
Add logo or text as watermark on top of image
Upload worse quality video
Mirror the image vertically