Excellent references, all...
Being a Linux user, the Sword project is my only choice for such things and their
Java interface is interesting, although not as easy to use.
I would love to have tonnes of footnotes and references available. I would love for a version that contained the texts of all the major religions and would let me compare things like references to the same historical event, compare timelines, etc. If there were footnotes/references to secular texts that cover the same item would be icing on the cake.
For that, my friend, you'd have to study archaeology. Cross-cultural historical cross-referencing is not a pretty thing to dig into, and those who have find the going very difficult, as the existing historical record is fantastically spotty.
I found
K.C. Hanson's website to be a nice jumping-off place, as he has links to many other historical archaeology sites and current translations of many ancient records.
Being Catholic, his focus is on the ancient mediterranean (Greece/Rome, Egypt, Middle East) so I didn't find much pointing eastward or westward from there.