Wow Great Pics!
Lee w/ only 3 effects pedals! heh... those were the days.
looks like a crybaby wah, and the other 2??? one looks defintly like a Boss (maybe the compressor listed on Chris Lawerence's Gear Site) maybe the Digitech 2 second delay/looper is the otherone, i don't know what the Fender delay he was know to be playing back then looks like as its hard to come by these days) and wow looks to be no distortion or overdrive boxes... they must've relied purely on the amps to do this, because in those other photos it appears Thurston doesn't use any pedals, but then there isn't any photos that clearly show the portion of the stage where they would be except maybe this one:
which is another great shot of him playing the eterna guitar and in the background at stageside the line of guitars, most of which were probably stolen in 1999...