pgfplots figures in publications

Actually, thanks to percusse's comment, I researched the pgfplots' externalize library and found that adding these two lines

\usepgfplotslibrary{external}
\tikzexternalize

to my preamble did just what I wanted for no effort at all!

(Ryan's answer is also great, and thanks to him, but this is a better way.)

One possible workflow would be to drop each pgfplots figure or tikzpicture: into a standalone document, which would give you a .pdf file of just that figure, which you could then convert using something else.

\documentclass{standalone}
\usepackage{pgfplotstable}

\pgfplotstableread{
    Ma       Mb      a
    200      50      5.6
    170      80      3.3
    140      110     1.0
    100      150     -1.6
    70       180     -3.9
}\caseone

\begin{document}
    \begin{tikzpicture} 
        \begin{axis}[
            title=Variable Net Force,
            xlabel={Acceleration},
            ylabel={Net Force},
            legend entries={Raw Data,Line of Best Fit},
            legend style={at={(0.973,0.03)},anchor=south east},
            width=\textwidth,]
                \addplot
                    [only marks, black] 
                    table[x=Ma, y=a]{\caseone};
                \addplot 
                    [smooth, black, very thin]
                    table[x=Ma, y={create col/linear regression={y=a}}]
                    {\caseone};
        \end{axis}
    \end{tikzpicture}
\end{document}

The above would output just the plot in pdf format, which then can be converted to anything and including it with \includegraphics would work fine because the whitespace is trimmed.

If you're on a unix-like system you could then use ImageMagick Convert to convert all the images at once, for example if you named all your figures figure1.pdf figure2.pdf figure3.pdf then you could use convert -density 600 figure*.pdf figure*.eps to batch-convert them all, preserving numbering.