I was just reading about this in Mike Holt’s NEC 2008 Changes book. He says that this requirement has no effect on conductor sizing if you bundle nine or less #12 or #14 current carrying conductors using the 90-degree ampacity for THHN conductors in Table 310.16 at 70% adjustment in Table 310.15[B][a].
This is probably more wires than most electricians would run through the same holes anyway, so shouldn’t be that big of a problem. It should have no effect on doubling up NM cables under the same staple either since that would be less than nine conductors.
I can see the need to address the issue of maintaining spacing between conductors though when more than nine conductors are run through the same stud bay or ceiling area, such as when running home runs from a panel. This should really be much of an issue for most of us to apply in the field.