I've done something similar (but much more simple), but this article has some interesting points. Now if only MathWorks would fix that stupid bug that showed up with the latest Java update.
Here's what I do: it scales the fonts and figures (using hgexport) and markers so that they show up as not to small a size when included as 3-inch figures, changes the font to Times, makes the minimum line width 0.5 points, exports to EPS, and uses the epstopdf tool to convert it to a pdf (since Matlab's pdf export is buggy and always puts the image on an 8.5 x 11 page). The results look consistent and very clean.
exportNiceFig.m
UPDATE 11/30/2008: I fixed the behavior of some of the resizing when there are multiple axes on a single figure.
UPDATE 01/21/2009: For future updates, see the projects page
30 September 2008
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