I'm not exactly a Biblical scholar, so Gaga's song "Judas" doesn't make much sense to me.  But, that isn't to say it has no meaning.  If you ask Gaga, and someone did ask Gaga, she'll tell you that the video isn't meant to be "a religious statement. I view it as social statement. I view it as a cultural statement. It's a metaphor. It's not meant to be a biblical lesson."

It took a commenter from one of the websites in the Gawker network to clear up the meaning of the song for me:

The lyrics "When he comes to me, I am ready / I'll wash his feet with my hair if he needs / Forgive him when his tongue lies through his brain / Even after three times, he betrays me / I'll bring him down, a king with no crown" refers to first to John 12:3-8 in which Mary anoints Jesus' feet with perfume and washes them with her hair. Judas asks "Why was this ointment not sold for three hundred denarii and given to the poor?" not because he cares about the poor, but because he is in charge of the money and greed had gotten the better of him.
Meanwhile Judas has plotted to betray Jesus and deliver him to the Romans. Jesus, aware of Judas' previous and impending betrayal—that he will die the next day at the hands of the Romans—says, "Leave her alone, so that she may keep it for the day of my burial. For the poor you always have with you, but you do not always have me."

The "after three times, he betrays me" lyric references Jesus' "one of you will betray me" line of questioning at the last supper Simon followed by Peter's 3x denial that he was Jesus' disciple when asked during the arrest before when Jesus explains "before the rooster crows, you will disown me three times!"

The lyric "I'll bring him down, a king with no crown" can be interpreted as Mary Magdalene's participation in Jesus' deposition (removal from the cross) in which she was joined by The Virgin Mary (Jesus' mother), and Mary wife of Clopas (his aunt).

All of this means that when Gaga/Magdalene says "I'm just a Holy Fool, oh baby he's so cruel, but I'm still in love with Judas, baby" she means to reference a desire to be pious and virtuous, but an attraction to greed, iniquity, and vice.

FINALLY Gaga references Magdalene's misidentification as an adulteress and repentant prostitute (suggesting Gaga's own casting as a whore for embracing her sexuality while celebrating her empowerment): "In the most Biblical sense / I am beyond repentance / Fame hooker, prostitute wench, vomits her mind / But in the cultural sense / I just speak in future tense / Judas kiss me if offenced / Or wear an ear condom next time"

Honestly, I still suspect that a Catholic school upbringing could be required to really get the full meaning of this one.  About half of the video was officially released by Gaga after the leak earlier today, but the full 10-minute premiere is still happening tonight on E! at 6 p.m.