Anonymous struck down government and industry Web sites yesterday in the biggest Anonymous operation in their history.

After the take down of MegaUpload and arrest of those associated with the sharing Web site, Anonymous, as we reported, took down the Justice Department’s Web site. This snowballed into the taking down of multiple sites across government and industry including sites belonging to the FBI, White House, MPAA and RIAA.

Anonymous confirmed through one of their multiple Twitter accounts and a press release that OpMegaUpload saw 5,600 people taking part in the take down of these sites.

The Web sites that Anonymous took down were justice.gov, MPAA.org, UniversalMusic.com, Anti-piracy.be, RIAA.org, FBI.gov, HADOPI.fr, Copyright.gov, UniversalMusic.fr, ChrisDodd.com, Vivendi.fr, Whitehouse.gov, BMI.com and WMG.com.

The group said that this attack was in part retaliation to MegaUpload being taken down, but they say that the larger issue is the federal government’s ability to enact take downs of Web sites without SOPA or PIPA being signed into law.

The darker side to all of this is that Anonymous were posting links throughout the night to their LOIC, or Low Orbital Ion Cannon. This software allows users to join in a DDoS attack. Previously, links to the LOIC would be voluntary and people could choose to join in knowing that participating in a DDoS attack was illegal. This latest operation saw Anonymous posting links on Twitter that would instantly launch a DDoS attack from the person’s computer without their authorization.

SiliconRepublic spoke to a consultant for Sophos Security and he said that users who clicked on the links without knowing it was the LOIC could still be prosecuted for the illegal move.

This move by Anonymous could be seen by some as invalidating the goodwill created by Web sites like Wikipedia on Wednesday that moved lawmakers and other supporters of SOPA/PIPA to the Internet’s side.

Do you think that Anonymous’ actions were justified? Will they have a negative effect on the dialogue in Washington? Tell us in the comments.