Bulldog, I think that it is really less important as to how you do it, than that you compare apples to apples. If you take the measurement standing, always take it standing, or visa versa. IMHO I feel that sag numbers can be manipulated up and down to meet your individual needs.
Start at 100mm (measured however you like), then try increasing and decreasing until you find the spot that works for you. I know tuners who never check sag, they go exclusively by spring length and rider feel. Don't get too caught up in it.
I personnally like the standing measurement, as it gives at least some consistancy to the measure (that is hardly precise at the best of times).