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PDF works OK if you set the output size to the Reader's screen size. If you don't need illustrations though, use RTF - very easy to work with and the Reader processes it very quickly.
If you want to get it looking exactly how you like, with tables, illustrations, etc, you'll want to use the proprietary Sony LRF format. There's some public domain tools that will generate an LRF file - just search the forum and you'll find the relevant threads.
If your reference books are in some format that you can re-size/re-flow the Reader might work for you but, as flumbo pointed out, its real focus is linear reading.
I'm not aware of a limit on the number of bookmarks per book. They show up in the bookmark list as a number and a couple of lines of text above and below where the mark is set. If you want to limit what shows, you can put a page break before the bookmark, then you just get the first line after the bookmark. The Reader supports linked navigation in PDF's and LRF's, but exactly how that works is still a matter of debate.
You can show either a list of bookmarks in a particular book, or a list of all bookmarks in all books.
If your reference books are hard-coded for 8x11, or use a lot of diagrams, you're probably out of luck. Try printing a couple of pages shrunken down to the size of the Reader to see what I mean.
You can type up your recipes as RTF's or, if they are relatively small (e.g. 3x5 cards), you could scan them to a PDF file as images. Either would work fine on the Reader.
Cheers,
Bob
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