Side note: The windows installer for LyX installs epstopdf (right, not eps2pdf 
or something else) by default along with the miktex LaTeX distribution.
It also sets the required converter rule automaticall (it's equivalent to what 
wvengen said, but LyX-win just does it like this):
EPS -> PDF (eps2pdf): epstopdf --outfile=$$o $$i

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lyx should recommend epstopdf for EPS support
https://bugs.launchpad.net/bugs/238580
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