Vanilla is a product of Lussumo:Documentation and Support.
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Let's assume you have a horror comic, and the monster is about to eat the hero, saying something like "Ooh, snacks! Does anybody have a ship load of guacamole?" This page would be entirely useless if you're searching for a guacamole recipe. So why have that word in the back end anyway? Aren't keywords like "man-eating monster" better?
The most SEO-friendly approach would be to use actual text for dialogue and narration (and an image per panel, with descriptive alt text). Unfortunately at the moment you'd be restricted to rectangular blocks of text, though with HTML5 we might be seeing that loosen up a bit.
I doubt that many people would want to go that way unless you could use the same source material for both the web and print versions.
From that XML repository you can generate a print-on-paper book, an ebook, or a page of HTML by applying an XSL transformation. Similarly images can be resized on the fly and converted to appropriate file formats (most server-side languages can do this - PHP uses phpGD or ImageMagick) so that they are suitable for the use in question (high-res TIF/EPS/whatever for print, screen res JPG/PNG for webpage etc).
As to HTML/CSS3, you're probably right, but I was thinking about the canvas element as the real New Thing.
Talking to Amazon, I got the impression they really want you to focus on the platform rather than on the device specifically. But with so many Kindles out there that bears some thinking about, and there are other technical issues to sort through. Honestly, I'd love to support them, though.
I did notice they have a bunch of IDW stuff in the Kindle store now that I've been meaning to take a look at.
I still say it's only a matter of time before we see higher powered Kindles and Color ones to boot-- but that time might be longer than I think. Besides that, I have to admit, what it does (read books) it does very well.
Mike didn't mention anything about the 64k limit on his writeup, so hopefully that's something they've gotten around. If I find out more, I'll report back!