To convert EPS files used with latex to PDF for pdflatex:
ps2pdf -dEPSCrop -dAutoRotatePages=/None filename.eps
ps2pdf in my experience does the most precise conversion. -dEPSCrop option is needed to prevent ps2pdf from outputting a full A4 page.
More control of ps2pdf:
All Ghostscript options (call with -dOption): http://pages.cs.wisc.edu/~ghost/doc/AFPL/6.50/Ps2pdf.htm#Options
To batch process a whole directory:
for FILE in *.eps
(This code is to be written to a text file, which is then made executable and run.)