Black wax/crayons have always been good for filling the occasional small gap. I actually have a wax filler set, but rarely use anything other than black. If it is more than a small fingernail width gap, I would patch/fill with wood. I will glue in wood shavings or wood dust and glue for slightly larger gaps than I would fill with wax. The wood filler will take stain but it will still be darker than the surrounding wood. This may or may not be a problem depending on if your are going to age or not. if you need as close to perfect as possible for an as new presentation, then putting matching wood patch in the inlet is the way to go. You just need to fill the part of the inlet with the gap and then re-cut the inlet in that place once the glue has dried.
Like Gaekle, my preferred method of fixing an inletting problem is to stretch the metal if I can. I always do this with the butt piece, brass and iron. I frequently end up doing this with the barrel tang. I have even done it with a lock plate. With the thinner inlays, you pretty much have to patch the wood. I don't think you can effectively stretch anything thinner than 1/16". If you have to hammer brass or silver much, anneal it after a few hits.
