While preparing the camera ready version of a paper, I had to upload the PDF file to IEEE PDF eXpress for validation. The validation service threw the following error at me

Font Helvetica, Helvetica-Bold, ZapfDingbats is not embedded (300x on pages 2-4).

There was, to me, no obvious way to fix it and their online documentation proved not helpful either. I tried a few avenues, but in the end I settled on a solution using Ghostscript. This was the only one that properly solved the issue and (seems to have) left the rest of the document intact. I found the solution I ended up using via Stack Overflow and provide it here. The Ghostscript command to use is

gs -q -dNOPAUSE -dBATCH -dPDFSETTINGS=/prepress -sDEVICE=pdfwrite -sOutputFile=output.pdf input.pdf

I will admit to not having delved in what each option means as I was getting annoyed with the process. This should however automatically see which fonts are missing and embed them in the resulting PDF file. Note that you may need to use the -sFONTPATH option if the fonts are not available in a standard location. See 1 and 2.

Update: To list the fonts in a PDF file (as well as whether or not they are included in the PDF), you can use

pdffonts file.pdf