John. This is a topic of great interest in popular history, but I tend to not use it much or use it at all even though it is in the heart of my major course of instruction, Twentieth Century history.
The reason I tend not to look to closely at this is that I find it difficult to argue historical significance of the assassination itself. There is not a clear story line from the assassination to show any group on the historical radar getting great benefit out of JKF's assassination (other than the laws JKF supported that got passed in his name under the Johnson administration.
That aside, this looks like a great website. Have you considered trying to design webquests as part of your student activities? In your case you may have provided too many resources for an off site web quest but you create a wonderful and contained environment for them. I am relatively new to webquests and love the idea of them but have yet to try to use a free form one. I do have access to a mobile pc lab to use fro my classes.
From looking at your material, one thing I might do with our lab on your site would be to ask my students to rank the assassination theories from most to least credible and provide reasoning as to the order.
Time being short in my classes I would probably ask for a top three list or a most believable and least believable scenario and ask for solid reasoning behind any ranking assigned. (Spellcheck arriving soon?

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Edited for a misspelling of the word spellcheck. LOL
Also to add.
I have forty five minute classes, if I do an exercise on this I will have to confine the activity more than I listed above (although they would work if I was to expect the effort to be homework as well.
I am thinking of trying it out this Friday because I am unlikely to get much done and I am presently on the 1960s in the US in my course.
I would have to make the students:
Pick a theory or be assigned one
Make a document that explains the basic theory.
Pick the most credible piece of supporting evidence (quote and or explain)
Pick the least credible piece of supporting evidence (quote and or explain)
Cut and paste some bio information from a key player they had heard of
Cut and paste some bio information from a key player they had not heard of
Make a brief conclusion about the theory
Then turn it in at the end of class (as long as the printer is working I guess.
It would be a race, but I think I could expect this much work.
BTW would the cut and paste stuff violate your terms of usage for the site?????