I'm thinking of building a pedalboard and I'm wondering what my options are for fixing my pedals to the board (which will probably be made of wood) I'd prefer not to use metal clips as I don't want to scratch the cases of the pedals. Any thoughts?
just get a sheet of padding stuff (like an inch or so thick from a DIY store its cheap), find a suitably sized sheet of wood to put it on, then lay your pedals out on the padding in the way you want them then cut out the shapes so they fit in to it, and lastly then stick the padding to the wood. job done and you dont need to fix or stick anything to your pedals.
Fender American Deluxe Ash Stratocaster (2000)
Fender Classic Player 60's Stratocaster
Marshall JCM900 100w head & 4x12 cab

Korg DT-10 Tuner; Boss DD-3 Digital Delay; Jim Dunlop JH-1B Wah; Boss RT-20 Rotary Ensemble; MXR EVH Phase 90.
Well Velcro sounds like a possibility, the only think I don't like about that idea is that I might end with a load of gunk on the back of the pedal, which might make them harder to sell if I decide to sell them.

ArcherTheVMan: I thought about doing something like that with a bit of foam, but I'm not sure what type of padding you mean and I'm also wondering if the pedals would fall out if the board was being held at an angle, though I guess you could cut the slots so they were very tight around the pedals.