Pitch shifters first (Whammy, octave shifters (except octave/fuzz units...those go with the gain units), etc)
Then my wah pedal...BUT if I use an envelope filter/follower or an auto wah I put that AFTER the gain units and before the modulation effects...
Then I go to gain units (OD, boost, distortion, fuzz, etc)
Then modulation effects (chorus, flanger, and I even put phasers here too)
The I move on to delay and reverb...
Also, I put tremolo pedals in with chorus, flanger and phaser pedals
Now, thats just the way I do it and thats not the way I do it all the time but I think it's pretty good rule of thumb...