"How do different departments compare when looking just at job prospects after finishing a PhD? Does it depend more on the advisor than the dept, or more on the individual? Any real life examples would be great! "
I got my B.S. in Chemistry from UC Santa Cruz and my Ph.D. in Chemistry from USC.
UCSC has an AMAZING undergraduate chemisstry dept. Because it is relatively small compared to, say, UC Berkeley there is heavy Prof./Advisor student interaction. I had two great years of research as an undergrad, and it made me a much stronger grad student. The grad program is very relaxed, but is doing some amazing research. You will enjoy your TA years there.
Santa Cruz campus is amazing! If you want more insight into the grad program, contact Dr. Bakthan Singaram, Professor of Organic Chemsitry. He is incredibly helpful. Tell him that Kim sent ya.
As far as picking grad. schools, go look up some journal papers on topics you are interested in studying, and see where the professors are from. This is how I decided on going to USC.