As RicodJour said, underlayment nails (ring shank) are good. Try and
pull one out that's been driven in correctly. If you do use screws,
1-1/4 should give you penetration just through the subfloor (3/4
subfloor + 1/4 plywood + 1/4 penetration).
I often use Phillips "Green" screws.
- Won't rust / Won't strip / Won't snap
For these, Phillips makes a bit (used to be included in 5lb boxes) that
locks in them very nicely for torquing to countersink.
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