My solution to this misery has been to glue another row of pin headers directly outside the mis-spaced ones, leaving one pin blank and connecting the offset pins "diagonally", somewhat like this:
oooooooo*oooooooo
\\\\\\\\ ||||||||
oooooooo.oooooooo
That way I can continue using "standards compliant" shields, or simply make my own perfboard shields (which will be 2.54mm or one pin row wider than standard shields, but have an even spacing).
