I use Xfig to do the diagrams in my papers. It's simple, clean, industrial-strength software, and exports cleanly to .eps files for inclusion in LaTeX sources. By default, text is in Times-Roman which is fine for papers, but not for slides. Since both .fig and .eps files are textual, I wondered if I could just edit them directly to change all the fonts at once to Helvetica. At least in this case, I could:
sed -i -e's/4 0 0 50 -1 0/4 0 0 50 -1 16/g'
sed -i -e's/Times-Roman/Helvetica/g'
(You may have to inspect your particular .fig files for the right regex.)
Relatedly, including .eps files in pre-2010 PowerPoint doesn't work well, so I used this script to convert them to high-resolution .jpg files. It bloats the .ppt file some, but looks perfect. You might be able to get away with a 300 DPI density instead...
#! /bin/tcsh foreach i ( $* ) convert -density 600 -quality 75% -colorspace RGB -antialias $i `basename $i .eps`.jpg end