YouTube has begun removing more than 100,000 unauthorized clips belonging to Viacom. The clips include everything from snippets of Jon Stewarts “The Daily Show” to Nickelodeons “SpongeBob SquarePants.”

The purge comes after Viacom demanded that YouTube take down the material, accusing the site of violating its copyrights. Viacom says its the largest order to delete videos it has ever made.

The situation highlights the growing challenges that YouTube will have to face to secure a viable future. Google’s $1.65 billion acquisition of YouTube showed that there was value in YouTube’s collection of user-submitted videos. It also made it clear to copyright owners that there was money to be made online from their content.

Viacom, whose properties include MTV, Comedy Central, BET, TV Land and Nickelodeon, said it spent months negotiating with YouTube so that it could be paid for its material to appear on the site.

“YouTube and Google retain all of the revenue generated from this practice, without extending fair compensation to the people who have expended all of the effort and cost to create it,” Viacom said in a statement.

“Every content owner that is concerned about their videos appearing on Google Video or Youtube has to evaluate every single video on both services to check to see if their copyrights are being violated,” notes GooTube critic Mark Cuban. “As a copyright owner, to say its time consuming and expensive is an understatement.”

via SFGate