While "Physical Disk\%Disk Time" and "Processor\% Processor Time" are useful, I find "Physical Disk \ Avg. Disk Queue Length" and "System \ Processor Queue Length" much more informative, especially on a busy server. These two are some of MY favorites.
Good luck on your testing. I'm very curious to know the outcome as we will be weighing the decision of installing 2000 or 2003 on one of our new clustered SQL Servers shortly.