Organizing one's historical sources and the events, series of events, causal connections that they contain, historical interpretations of events from other historians (i.e. references and citations) into coherent narratives, arguments, historical hypotheses, all in clear prose that connects the author historian's intended idea up neatly and clearly to the non-specialist reader's understanding. Sounds complicated.
To my knowledge there is no specialized software for historians to write history with. Perhaps its even sacrareligious to suggest that such a thing could exist.
Certainly putting a software yoke over the historian's neck and not allowing her room to exercise his (or her) individuality and idiosyncracies wouldn't be acceptable.
Focusing on easy configuration of existing software tools and how they could be better employed in common everyday historian tasks would be a good start. Found this very relevant tidbit of info today:
"There is a new online Google discussion group for productivity in scholarly work. It is called The Efficient Academic. I don't know why, but my impression is that people in the academia is much more disorganized than the "business" people. We try to cover it as a source for creativity, but is it really a legitimate excuse? Is there anything we should learn from the business self-help books (like the excellent GTD)? It is nice to hear others' experiences, solutions and tools." (From: MIT physics student "Cabi's Glasses")
This thread on Managing Research Information was interesting including a reference to JabRef reference manager software, a "Java GUI frontend for managing BibTeX and other bibliographies".
The referencee to GTD is also interesting. It is apparently a "crash course in basic time management and personal organization" that almost wikipedia-like provides you with "fancy terms, subterms, and sub-subterms for even the simplest concepts...the spine of his system is captured on a straightforward, one-page flowchart that you can pin over your desk and repeatedly consult without having to refer back to the book.
I was looking for something like this when I posted Looking for open source bibliography software anyone?