It depends how much water I take out, if its just 10% I turn off nothing, @ 20% I turn off the Aqua One Canister, @ 30% I turn off any internal filters, and anything over 50% I turn off the Fluval FX5. The reason I do it like this is cause the filter is exposed or the intake isn't under water no more.
Many people turn their filters of cause they use those phyton things and if the filters are left on they kill off their BB cause the filters suck up chlorine. I for one am against using straight tap water to fill your tank, even if prime is being dumped in every so often as it fills.