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When I mentioned optimization, I was mostly referring to document formats which tend to make extensive use of layout features and such, like PDF files. Pages in PDF files are supposed to be a 1:1 copy of what you should see when that page is printed, either in a book or off your printer. It includes the white/blank margins around the borders of the page, the font size, the font weight, the graphics, etc. On top of this, most of the PDFs are intended for a larger page size, or even specifically for viewing on a computer screen.
So due to the flexibility of PDF and other document formats, a document intended for viewing on one device may not be best viewed on a different device.
If all of your books look and read fine on your reader, then you probably don't have to worry about it much, but if you have some PDF files that show up tiny on your Reader screen, or they fill up the screen fine but the font is too light/small, then there are ways you can modify the PDF files on your computer to make the text bold, get rid of the page margins and so on. This way you may be able to view those books on your reader without having to increase the font size or without having to zoom in, both which can be a hassle at times.
It is best if you can leave the font size at the default Small setting, because if you increase the font size setting on the Sony Reader, it will actually hide any images that may be on the book page and instead it will reflow the text to fill the screen. So if you need the images to be visible on the page, but also need the font to be more readable, changing the font size on the reader itself isn't an option and the PDF needs to be modified.
The general idea is basically just to make the book read and display fine on your reader without any or minimal changes. I don't have any links handy, but here on the forums there are links to programs and methods you can use to remove the margins and embolden the text of your PDF documents if you have any.
Also, if you have any photos you've taken with your camera that you want to display perfectly on the Reader, those can be optimized too by scaling down/cropping the image to the exact screen size of the Reader. This way the reader won't have to resize the image on the fly which should keep it sharp and on top of that it will be a smaller file size, so they will load faster as well as take up less space on the Reader, allowing you to store more.
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