Can spar stresses be calculated using zero (wing) fuel? For a homebuilt prototype aircraft meant for the primary or Canadian JAR-VLA category, is it OK to assume that spar stresses (other than landing loads) can be calculated using zero-wing-fuel numbers? Or perhaps the landing loads usually negate that zero-fuel stress relief?

So, when specifying plus and minus stresses, both the wing and its fuel content can be discounted except for full-fuel aileron loads?
In general, combining an empty wing with a full fuselage will give the highest stresses in the wing spar at positive and negative load factors. If the wing tanks held fuel, the weight of the fuel mass would reduce the wing spar bending moment inboard of the tanks at the same load factor.

However, details depend on the particular configuration. Make also sure you look at the most forward c.g. location and at the added load from aileron deflections.

Also, don't assume that the critical load case of one design will also be the critical of another. Please look at cases in all corners of the envelope to make sure you do catch the critical one.