I've been talking for a while about the best way to do referencing in the era of the ebook. Well as of calibre 04.99, the ebook-viewer has my first stab at an answer. You can enter the "reference mode" In that mode mousing over a paragraph will give you a number that you can use as a reference. You can type reference number in the Go to box to navigate to them.
In addition 0.4.99 brings support for bookmarks and user stylesheets.