I have been reading Supertraining by Mel Siff and I am pretty sure that it said to count everything over 60% for advanced lifters and anything over 40% for beginners.
My two cents: I do what Mike said and basically count my "working sets". Different systems have you counting total volume, like Andrew said, starting at lower percentages. Sheiko templates, for example, count everything from 50% and above. The one thing I didn't care for with Sheiko was the number of sets done below 80%. I got conditioned but I've never been big on doing many sets before my working weights.
my amatuer opinion is that sets should count once that hit an 7 rep or better. In sheiko there are sometimes alot of sets before you reach the top weight. So say for instance that you do alot of sets at 50 and 60 percent and then you get to 70% and it feels like an 8 rpe but your goal percent is 85, so in this case I would definitly count the sets at 70 (although I do agree that you should count them all for tracking purposes) since any set that's working at an 8 is definitly a work set
this whole idea of doing more sets at lower percentages is different than the generic rts programing and the 10% method is probably great for the more generic version but if you deviate from that method you may want to consider counting the sets based on the rpe of the set