For inlays, I have a few bags of sawdust I collect and make some filler to match the wood that the hole is in. This may not always be true, but I've found that if I drill the blade entry hole closer to the darker colored wood, I can usually hide the hole pretty well. As for fretwork, I do like grampa and make a teardrop shape. When I make bowls, I just sand,sand, and sand until the hole disappears.
Dan