Zippy - ?
When Trinity and Neo shoot up the Lobby, its a custom mix of "Propellerheads - Spybreak" that plays. (I wish I could hunt this down... the version in the movie isn't the one on the CD. Bummer.)
"Wake Up" is played at the very ending of the movie, during the (crappy) ending, where Neo yacks at the AI a bit in a phone booth and then flies away.
And yes, it's the same riff, but both parties know, so its cool.