If your images are in pdf you can use the convert tool in imageMagick like:

convert -density 300 in.pdf out.jpg

For the record, this is the command I happened to use to convert pdf figures to tiff suitable for submission to PlOS One:

convert -alpha off -trim -resize 1180x1180 -density 300 -depth 8 -compress lzw fig.pdf fig.tiff

Options explained:

-alpha off : Turn off transparency of background (Plos doesn't like it)
-trim      : Remove unused/white space around figures.
-resize    : Resize to i x j pixels. If the source image is not squared, make the 
             largest dim (h or w) these many pixels and 
             the other dim smaller. I.e. proportions are conserved.
-density   : Density as pixels/inch (DPI).
-depth     : Default 16, Plos wants 8
-compress  : Compression algorithms. lzw, required by Plos, makes the image much smaller!