Personally, I'd like a DJVU and PDF viewier that lets you highlight regions of pages and create hyperlinks to other pages in the same document. It should also have a history feature that gives you back/forward functionality like a web browser, and the focus should be on making it easy to read or refer to books and documents that require a lot of jumping around.

I'd especially like one that suggests hyperlinks for documents based off of what users typically make hyperlinks for or based off of some kind of algorithm with heuristics built on content and formatting conventions, because even though just being able to create your own hyperlinks would be handy for studying and reviewing, having them appear magically would be a killer feature.

However, that'd probably be too hard for a single weekend. For one thing, it'd still have to be a good PDF viewer, which means nice features like being able to custom crop/zoom pages to hide margins in documents with lots of extra white space, and it'd have to perform well with the large, complex kind of documents that people would want to add hyperlinks to.

It also lacks long term viability due to the slow rise of eBooks with hyperlinked content on delivery platforms like the Kindle.