Judas Iscariot was one of Jesus' twelve apostles. Judas betrayed Jesus to the Romans.
It's been postulated that Judas in the context of The Hold Steady is another name for Holly, who, in Both Crosses, may betray Charlemagne (who, as you'll recall, she thought was her savior) to his death or near-death.
See Also: When judas went up and kissed him
from Chicago Seemed Tired Last Night, Citrus and Both Crosses