a) Scatter lots of GPOs around an OU hierachy each with specific sets of Preferences relevant to a given OU branch.
b) Just have one or two near the top of the hierarchy, with settings for everything way down below but using conditional targeting e.g. set A if user/computer belongs to OU X, set B if user/computer belongs to OU Y.
[..or "belongs to group X"]
Anyone deeply enough into this yet to have strong opinions about the best way to go?