Tracking the course of evolution: Presentations, from origin of life to cladistics
http://www.ucmp.berkeley.edu/education/events/presentations.html

Introductory courses to Human and Primate evolution, and more at Palomar College. Very pretty.
at: http://anthro.palomar.edu/

Organic Evolution by Rebecca Irwin (The University of Tennessee at Martin). Introductory level course with hand-outs.
At: http://www.utm.edu/~rirwin/evol.htm

Advanced course at Marine Biology Laboratory. Not a real on-line course, however, some hand-outs are freely downloadable. At: http://newfish.mbl.edu/. Go to mainpage, and follow the links to "courses".

Neat Molecular systematics and evolution course at the The Natural History Museum, London. Downloadable lecture notes in pdf or ppt files:
http://www.bioinf.org/molsys/lectures.html