This has been discussed many times. Some searching the archives should yield information on what some do...micro branding irons, engraving on the back side of the clips, marking on the transmission of ballpoints, I know a couple of guys who have their own laser engravers and engrave very small ID marks and a couple who engrave their (small)signature around one of the barrels on the end.
One thing I wish I had done, but it is way too late for me, is to take a picture of each pen and design a spread sheet with the picture, kit info, material info, dates and where the pen is now. There are a couple of pen specific data bases available for doing this. It would be interesting to look back over the years and see where my opens have ended. Just saying.
Do a good turn daily!
Don