For a 2000 LE like mine I have uncovered the following parts for power windows (plus parts categories and price from 1sttoyotaparts.com):
Window Motor (Electrical , Body electrical ,Front door ,Window motor)
189.56
Window Regulator (Body hardware , Door ,Front door ,Window regulator)
56.36
Window Relay Marked 9008498031 (Electrical , Body electrical ,Door ,Window relay)
37.53
Window Relay Marked 9008087010 (Electrical , Body electrical ,Door ,Window relay)
15.47
Isn't it possible to short out this stuff when driving in the rain? I also have been guilty of using the rubber stripping between which the window rolls down/up as a squeegie! That too could have done it!