Does pedal order affect your sound if you only use one pedal at a time?
e.g. Let's say you have a Boss SD-1 and a Dunlop Wah Wah. If I order it SD-1 into the Wah, and only use the SD-1, would it sound different if I put the Wah first in the chain?
Arguably not, no. Unless you're using them at the same time, it won't make a difference.
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I've tried my pedalboard in many order. It does sound different. I don't think the crowd could notice from one configuration to another but hey, it's the addition of all the decisions you make that draw your sound.

True bypass pedal does not really impact (if not at all for some) the tone. However, buffered output pedals like a Wah will create a noticeable tonal change.

Also you have to ask yourself, do you want to overdrive the signal before it comes into the wah, or after?
It can have an effect. Some fuzz pedals sound different if a buffered pedal is before it. It's all a matter of testing.
It can, depending on the quality of buffer (if there is one) or true bypass.
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Quote by Gheymix
Does pedal order affect your sound if you only use one pedal at a time?

It certainly could, wahs are generally picky about buffers and impedance so you might notice a slight difference. Usually it's more noticeable with fuzzes or digital pedals but it might not like being after the Boss.

Why don't you try it yourself and see? You've only got two possible combinations, it can't be that hard to test.