MIMF

I'm just about finished with the neck I've been building and I was wondering what ways people apply logos/insignia to the custom builds.

I know that using adhesive transparency paper is a common method but are there any other ways? Some sort of pen? Paint? Etc

Thanks

The three common methods (although the last isn't exactly common these days) are Shell inlay such as Gibson, Waterslide Decals (available from many places and customisable) such as Fender or a separate logo cut, carved or engraved and attached to the headstock. pens and paints can react with your chosen finish so you would have to check for suitability before applying I would say.

+1 on waterslide decals. They're easy and look great, especially on light finishes and especially under a clear coat. There are some folks on eBay who will customize them for you at a pretty low cost.

I've used Sharpie marker pens over nitro lacquer with good results. I believe Melvyn Hiscock features this method in his book.

I've also used transparency sheets. While the printing came out really sharp, the sheets have a thickness that's hard to hide.

Check out John Kingma's headstock. I think they are really cool.