(Summarising the comments as an answer.)
pdfTeX will work with px units, but you have to set these up appropriately using \pdfpxdimen. This is the physical width of one pixel, and has default value of 1 bp, meaning that images initially are assumed to be 72 dpi. \pdfpxdimen is a low-level dimen primitive, and so is best set using \dimexpr:
\pdfpxdimen=\dimexpr 1 in/<dpi>\relax
where <dpi> is the resolution of the image.
With that set correctly, you can then use \includegraphics as normal, adding px to the values used by the trim (or other) key to get the right result.
As an example, consider the two images

and

which have the same pixel size but different resolution. Using the LaTeX file
\documentclass{standalone}
\usepackage{graphicx}
\begin{document}
\setlength\fboxsep{0 pt}
\pdfpxdimen=\dimexpr 1 in/600\relax
\includegraphics[clip,trim=0 100px 200px 100px]{Figure-a} % 600 dpi
\pdfpxdimen=\dimexpr 1 in/72\relax
\includegraphics[clip,trim=0 100px 200px 100px,scale = 0.12]{Figure-b} % 72 pdi
\end{document}
results in the output file

which shows the result of the trimming - both are the same. (I've scaled the second image so that the two are printed the same size by pdfTeX.)
pdflatexsupportspxas length unit. Did you tried using\includegraphics[clip,trim=0 100px 0 0]{image}? – Martin Scharrer♦ Jun 27 '11 at 16:42\pdfpxdimen=\dimexpr 1in/300\relaxshould do. The default value of 1px is 1bp, i.e., the default resolution is 72dpi. – egreg Jun 27 '11 at 18:04figureenvironment, for example) the setting will be restored when the group is closed. Or say{\pdfpxdimen=\dimexpr 1in/<res>\relax\includegraphics[...]{...}}. – egreg Jun 27 '11 at 19:14\pdfpxdimen=\dimexpr 1in/96\relaxin the figure environment for the first image and\pdfpxdimen=\dimexpr 1in/300\relaxfor the second, then apply a trim of 100px for both, shouldn't this perform a nearly identical trim on them in the final document? Because I tried this and it's clearly a different though similar level of trim. Too big a difference to be rounding error at the pixel level I think. Thanks. – SSilk Jun 27 '11 at 19:24