Here is an index of all the lecture notes available on this site:
Quantization and Categorification (2003-2004 academic year)
Gauge Theory and Topology (2004-2005 academic year)
Quantization and Cohomology (2006-2007 academic year)
Classical versus Quantum Computation (2006-2007 academic year)
I took these notes in real time, during the seminar, and then usually fixed them up a bit before scanning them in. Fortunately John makes a point of being easy to take notes from, which made my task considerably easier than it would be in most lectures. The notes are a mixture of what John wrote on the board during the seminar, what he said but didn't write down, and sometimes whatever I interpreted him to be saying.
(All of these notes, plus notes from other quarters in the seminar, are also available from John's seminar page.)