If I had to list a villian who could do the most damage to us alone that would last the longest, Xana and his hacking would definatly take the cake, if he ate cake that is; Thomas
XANA is a horrific computer program from Lyoko. It has the ability to possess tech, plants, animals, peope, well its isn't fun to be around this, thing. Xana has a army of monsters at its command, virtual beings it can sometimes materialize onto the main world. It has an obsession with killing, memory depriving and possessing Aelita.
XANA, possessing William, battled Thomas in Lyoko as it was destroyed. XANA was destroyed by Thomas, with Po's wushu Finger hold. Later Kronos brough it back, and its monsters are being put to good use.