If the holes are deep or in a crowded pattern, odd location or have an elliptical opening, I will use epoxy thickened with wood flour. You can tint the epoxy with "oil soluble" aniline dye. I've had good results using System 3 Gel Magic epoxy. The wood flour they sell is very fine and mixes in without being lumpy.
Even if you don't hit the tint dead on it will still look great and never be a moisture intrusion point.
Please throw me the bowline Fraulein!