The Campaign Builder's Guild

I'm thinking of something like Tiddlywiki or Zim desktop wiki - not built for collaboration and little overhead (no web hosting or the rest of that). I.e, the setting version on Obsidian portal is almot complete enough for a GM to run a campaign in and around Salis Freeport now. I'm wanting to put that on the GM's computer instead of a web host, with all it's hyperlinkage and more. The little personal wiki apps seem to be the way to go. Tiddlywiki runs in your browser and doesn't what browser or OS you're running. Perhaps other hypermedia apps will do this but I do want to avoid platform specific programs such as OneNote. I'm sure I can do this in Tiddly or Zim, I just don't know if either is the best choice or what others are out there. I'm also hoping to minimze editing after porting - copying pages from my CBG wiki to my wiki on OP requried a fair amount of edting since they have some different fomat/command structures.

I stand by my assertion that it's a bad idea. Even a "desktop wiki" is going to have a decent amount of overhead, because it's still an application. Computers probably won't complain, but lower-end tablets and smartphones might. Depending on how much Javascript it uses, some platforms might just refuse to run it; it seems Tiddlywiki won't run on a Kindle, for example. Since what you're providing is an application instead of just data, such incompatibilities become your problem, rather than using an existing e-book format where someone else is worrying about all that.

So what e-book format would you recommend that produces an interlinked, non-linear, easily navigable data array (which will run on Kindle as well as all the other proprietary devices that don't like to play well with each other)?

You'd need a different format for different readers. Depending on how you generate the ebooks, that could be very simple, or less so. Kindle can read .pdf, but it's primary format is .mobi. Most other readers use .epub. I'd think you could have internal hyperlinks in a .pdf. It would be non-linear in the sense that the user could navigate as desired, although one could, theoretically, just read straight through.