Wood filler is an easy way to fill pocket holes, especially if you plan to paint your project.
You can buy factory made pocket hole plugs and in the same species as your project.
Use Bondo to fill pocket holes. Use this method if painting your project.
Make your own pocket hole plugs from scrap wood using a pocket hole plug cutter.
Wooden dowels cost less than a bag of plugs, but require a bit more finishing work.
Use sawdust and wood glue to make your own pocket hole filler. The only cost is the wood glue.
Plastic pocket hole caps are great to use if you may need to take your project apart at a later date.