I don't know if it's paranoia or just habit, but I always put it first after the input. In my head, I don't want it being affected by drives or anything else that could potentially cause artifacts. Really, I've never even tried using the Virtual Capo anywhere else but right after the input, same for the Whammy presets I have, which is strictly out of habit because that's how I always ran my Whammy pedals. At most, I'd have a boost before it.
For any other pitch stuff, I generally put it in before any other effects if I'm doing it before the amp, or just between the amp and the cab. I really haven't messed with it much, outside recreating my previous physical rigs.