I like custom PDF's. If you use OpenOffice.org and any "Heading" styles, the headings are saved as the Table of Contents and can be used as quick links from anywhere in the PDF (Table of Contents entry in menu).
ePUB has been good to me as well. Unfortunately, it doesn't resize images if they are larger than the screen, but I just open the ePUB zip and resize the cover (or other images) myself. Irfanview can do easy batch resizes.
Note that you'll want firmware 0.33g for best formats support (including HTML).
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