I have never seen a Nikon users manual, but I can tell you that the manuals that came with my Canon XTI, and my Canon 5D both had a lot of very useful information in them. It is surprising how many people don't read them. These manuals detail how the different shooting modes work (AV, M, TV, etc), how to effectively use them, and what to expect from them.
Again, I am not at all familiar with the software that Nikon bundles with their cameras, but with Canon their Zoombrowser and Digital Photo Professional software is actually very good. I guess all I'm saying is that she should try what came with the camera before going out and buying something else.
As far as other sources of information; I personally have learned a tremendous amount at the Fred Miranda Forums http://www.fredmiranda.com/forum/
. I hang out a lot in the people forums, where photos are regularly submitted by members for critique. By using the search function in the different forum sections you can easily find information on different software, etc.
I'm sure she's going to get lots of good photos with the D40!