I would do a bit of research into the field of timber framing if your interested in structural wood joinery. I would also take a look at Japanese examples as well as they use some really interesting joinery. On a smaller scale using a shopbot to cut such joinery might be an interesting possibility. However full scale joinery on an 8x8 or 10x10 timber would of course present a number of difficulties and that would be the time to get out a large circularsaw and chain mortiser.
If you had to build a structure with nothing more than what you could carry in to the woods, a look at historic methods may give you the answer your after. After all 200 years ago if you were going to set off to build a house in the woods, you were probably limited to what you could carry on a horse.
Of course the more economical/modern solution may be to work with an engineer to design structural brackets/connectors to meet your needs.
Hopefully codes aren't too big of an issue where your planning to build.
Michael Schwartz - Waitsfield VT
Shopbot prs standard 48x96. Aspire. SB Link.