Have you ever used the Birnbaum guides (Unofficial Guide to Walt Disney World)? They have done extensive research and have published "touring plans" which denote the order in which to visit rides and attractions in order to cut waiting time. We tried it last year over spring break, and it worked beautifully. We never waited more than 20 minutes for any ride. They claim that during a busy time of year, following their touring plans can cut 3-4 hours of line time. Its actually pretty interesting to read (if you're a nerd like me) about how their research was conducted and the mathematical theories supporting it.
Jodie