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Originally Posted by wannabee
You answered your own question. (bold is mine)
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I would still be inclined to use hyperlinks, in addition to whatever workaround you come up with to enhance reading on devices that don't support them properly. Otherwise it is a least-common-denominator approach which will not be so attractive to the people using capable systems. And actually, I would not even worry about the incapable systems, they are going to die off soon enough, because that's probably not the only way they are 'unfit'.
That said, you might check out the 'ebook ninjas podcast' @ ebookninjas.com - I want to say episode 27/27b or maybe 23. There was some discussion of a sort of 'biblical' reference system, book/chapter/verse etc. — generalized in such a way that it could give a 'universal', format-neutral way of referencing a location. The reading system would be able to reveal/hide these references on demand, and allow some way to directly navigate. Of course it is all hypothetical, nobody has implemented such a system.