To embed type-1 fonts into a PDF document, run it through ghostscript:
gs -sDEVICE=pdfwrite -q -dBATCH -dNOPAUSE -dSAFER \ -dPDFX -dPDFSETTINGS=/prepress \ -dAutoFilterColorImages=false -dColorImageFilter=/FlateEncode \ -dAutoFilterGrayImages=false -dGrayImageFilter=/FlateEncode \ -sOutputFile=output.pdf \ -c '> setdistillerparams' \ -f input.pdf \ -c quit
Update: There might be another way: in the source LaTeX document, add these lines:
\RequirePackage[T1]{fontenc}However, this does not embed fonts used by PDF diagrams included into LaTeX documents. To deal with those, for each diagram file,
$ pdftops -eps Diagram1.pdf - | epstopdf -f > Diagram2.pdfand then run pdflatex again.