I am wondering if anything has been done as far as developing an open source solution to this. I would be interested in starting a project. My tools of choice would be eclipse and java - java for the ability to be cross platform and eclipse because that is what I am used to and I don't have a lot of experience programing. I have thought of a simple design, but would be very interested in some help to develop a program to accomplish at least some of these goals. I also wouldn't mind trying to learn C#, so long as it can be complied by mono - I run Linux as my desktop of choice so making something incompatible is not something I am interested in, but I would also like it to be compatible with windows and mac, since I know others have differing opinions about what they feel makes a good computer.
My idea would take the online scriptures (and possibly anything on the church's gospel library site) and format it such that it would be easy to read, study, and record thoughts with. It would strip all of the original html. It would allow for highlighting, underlining, and bookmarks, with each of these being able to be organized in a few different ways. I haven't thought of a particular way of having persistent online storage of customizations, or of sharing these with others, but I would want to have the design such that this would be a possible solution. As far as persistent storage of the customizations, I don't know if a database backend or xml files would be better or easier. It would also be possible to create your own footnotes to reference other scriptures easily.
That is an overview of my thoughts. I know it isn't an online solution, but I would like it to be something like f-spot - a stand alone program that works well by itself, but also integrates with online resources. I haven't really written any code for it yet, and wouldn't have time to start anything until the BYU semester ends, but I am interested in helping to make this sort of program.