HandBrake is an open-source, GPL-licensed, multiplatform, multithreaded video transcoder, available for MacOS X, Linux and Windows. It comes with a clean and simple GUI and allows for easy encoding tasks.
HandBrake is currently maintained in the official repositories.
HandBrake comes with predefined encoding profiles that might be well suited for most of the tasks. Yet there is no YouTube profile provided. If you want to encode a video to upload it on YouTube, choosing the MP4 format + Web optimised option might suit you best.