Judith was Maynard James Keenan's mother's name. She was a very religious person. One day she had a stroke that left her in a wheelchair partially paralyzed. This stroke only strengthened her belief in God - something that Maynard found to be pretty ironic. The lyrics in this song reflect how he felt about the whole situation - "It's not like you killed someone, It's not like you drove a spiteful spear into his side, You praise the one who left you broken down and paralyzed." He's saying that his mother was a good person who believed in God and yet this is how she was "thanked."
Krystle - Brooklyn, NY