hmm, that c&p into Word method isn't bad. I'll give it a try. I'll see if I can convert it to something other than PDF, though, since using even medium-sized fonts (such as the Reader's 'small' BBeB setting) comes out too faint (@#$@ sony).
kovidgoyl, thanks a lot for the htm to BBeB suggestion. That sounds perfect.
Henkvdg, I have a feeling that the reason SciAm looks good on the Iliad is that it renders the fonts right.* If I put the Reader into landscape, it effectively has more resolution than the Iliad but the characters are still very hard to read. Also, The Reader has only very rudimentary presets for zooming/rotating PDFs (not that panning is very enjoyable with eInk).
*In fact, if Iliad didn't want to pay Adobe for its software, they are probably using the same Ghostscript engine I am.
Anyway, I've noticed that inverting colors makes glare worse. Another thing I've found to work well is using the -unsharp 2 parameter in imagemagick. It essentially makes the letters bolder but messes with the antialiasing.
convert -unsharp 2 infile.*.png outfile.%03d.png
PNG - example 2e
I think even better image filters can be created. I know very little about this, but maybe somebody else does?