I've found that many of Protel's hole sizes are a bit small for my liking - in particular, the holes in their post header footprints are definitely too small.
I use .035" for most through-hole parts, and .025" for vias. Post headers need .040, and 1 amp diodes and larger electrolytic capacitors will need larger holes (and pads)
If the board maker quotes unplated hole sizes, you have to allow .003 or so for plating. When I order boards from the local shops, I specify finished hole size, and let the board shop figure out what drill to use (I don't know, or care, what drill sizes they have).
I would expect the board shop to translate between English and Metric dimensions as needed. There should be no need to create artwork and drill files in both measurement systems.