As always, there are no right or wrong answers as to what order is really "best" per se…it really does come down to what particular type of tones and sounds you're specifically after. 
For example, someone after a more traditional rock style of tone might use a totally different effect chain order than, say, someone who's going for ambient/textural soundcaping, experimental music, etc.
That said – I've always personally preferred to put my PitchFactor after any kind of distortion, overdrive, fuzz etc regardless of the style I'm working on at the time (I do a lot of ambient work as well as rock).
My reasoning for this is that I like to take the more "completed" drive/warmth/distortion tone and THEN pitch-shift it with the PF…otherwise I'd end up applying distortion to the pitch-shifted tone itself, which (again depending on what you're trying to personally achieve), for me usually tends to muddy the pitch-shifted effect and make it sound much less distinct.
For the same kinds of reasons, sending an already-distorted signal into the PF also gives it a very harmonically rich tone to work with, often with plenty of sustain to boot.
Another thing to consider is whether you're aiming at a sound with actual harmonies where the PF's tracking the original root notes is critical – if so, you'd probably want to avoid putting anything BEFORE the PF that would modulate the original tone's pitch and timbre, such as any kind of chorusing effects, dense reverbs, thick flangers, etc….doing so make it that much more difficult for the PF to cleanly ascertain what you're original root note(s) are supposed to be and then cleanly track it to generate the harmonies. In other words, it's hard to calculate what a major 3rd over a root D would be, if that root D's pitch is warbling and shifting like crazy. 
If that kind of thing is important to you, you would likely want to put any kind of modulation effects like that AFTER the PF.
But again – if on the other hand you're aiming for a more textural, experimental and/or ambient kind of tone….doing something like that might give you something interesting and unique! For example, for a lot of the dark-ambient work that I do, I'll often send my signal through reverbs, flangers, etc and THEN send it off into the PF….in that case, I'm not concerned about "perfect pitch tracking" per se, and often really like the resulting kind of unpredictable and sometimes glitchy tones it can provide.
