Some ideas:
For metadata removal only you could use jpegoptim too.
Similar could be done with SVG:
http://code.google.com/p/svgmin/
Ruben found out that extracting the SVG code from the file and inline embedding it directly into the epub makes significantly smaller files too. It would be worth to check back with Hitch how different reading systems react to inline svg code.
Are you recompressing with Zopfli?
AdvanceCOMP:
Advpng for the images;
Advzip for the finished epubs.
When I was digging for shrinking tools for Hitch I also searched for minification tools which could be applied to the epub's CSS and sources, but found only *. js stuff for use with webservers. Have no idea how to utilise it. Minification could be worth being looked up too.
Apart from that - what you are doing here: intelligent standalone tools for font subsetting; storage footprint optimisation (I'm a compression fan myself
) - what you do is exactly literally what I had in mind. It's development in the direction that matters. Bleeding edge, tailor made best possible epubs. Kudos and big big thanks for what you do.