Wow! That's a good collection if you have all of these. I'm sure Ms. "MJ Catalog" will have a thought on all this. But from me, I can say there are indeed different variations of a couple of the above books.
First off, there is the History variation mentioned above. I've never seen the "Eyes" cover on the Dangerous alternate version, so not sure where that may have been used. And then there are these, that I know of.
1) For the JVT tour book, there are two variations. The easiest way to tell them apart is via the back cover. The "close up" version was the one that was sold at Kansas City and maybe the next couple of shows, but it was later replaced by the other version (guess someone liked this photo better!). The other major difference is the color of the pages. The "original" version (let's call it the "Kansas City" version), has a blank internal cover page, where the more common one has the Victory album cover. Presumably, the KC version was printed before the Victory album was out, or at least before the artwork was finalized. Also, the fonts and page coloring is different between the two variations. The KC version uses purple whereas the more common variation uses blue.
2) I've never seen that alternate version of the 1988 Bad Tour book above, so not sure where that was used. However, there is a slight variation of this book if you look closely. Toward the back of the book, some of them have a "Smooth Criminal" video page in there. Obviously, at some point this was changed. My guess is this version is the newer of the two, because when the earliest of these tour books were used (again, starting with the USA Kansas City shows, since the 1987 Japan/Aussie books were different as you have them above) Moonwalker was not out yet (and it was never released in the USA apart from VHS anyway).
3) Like the UNCF book you have pictured, there is also a special "Prince's Trust" version of the Bad Tour book, that was sold that one show where Charles & Diana attended. The book inside is the same, but it has this special cover as I am attaching below.
4) And depending on how you define "tour book", there was a special "Japan tour booklet" for the Bad Tour, as pictured below. As for if this was actually sold at any of the shows, I can't say for sure. It may have only been included in the "Bad Special Box" CD box sets (which also included a T-shirt, etc.) and sold at the "Hello Michael" shops that were in Japan at the time.
And just as an aside, you would think that there were tour books designed and printed for "This Is It" although I have yet to hear about even any prototypes that exist (not that I've been collecting seriously very recently). Still, it's odd that any info on this was never leaked to my knowledge (although surely some scumbag bootleggers have had their own "versions" on Ebay).
Ron