Shameless plug: I put out jsmag in PDF, and regularly get people asking for Kindle version, but have not yet been able to make something look decent. Revisiting this again next month. Suggestions/guidance on this topic welcome.
I had good luck with formatting things for my Kindle with LaTeX. I just set the page size to be proportionate to the Kindle screen and compiled a PDF. The result was far better looking than using the normal Kindle format and I didn't have the normal issues with PDFs because mine actually fit on the screen.
This wasn't the most space efficient system, but it was probably the best one aesthetically. Also, since I just created a custom .sty file to automate this, I can have my single source document output both normal-sized and Kindle-sized PDFs.
Shameless plug: I put out jsmag in PDF, and regularly get people asking for Kindle version, but have not yet been able to make something look decent. Revisiting this again next month. Suggestions/guidance on this topic welcome.