I have a Starrett dial caliper that will measure to 1/1000" - now that
will let me have tolerances of about 1/100", which is heading in the
right direction but when I think about it, a piece of newsprint is
about 4/1000", or 1/250" and I know that my joints are tight enough,
when they are cut properly, that I can't fit a piece of newspaper into
them.

And yet, that can't be possible because the best measuring instrument
that I have in my shop will only allow me to have tolerances of
1/100".

If you mark one part of a joint from another, what's the error
associated with that procedure? Isn't this what determines the
accuracy of a joint rather than the ability to measure anything?
(I'm assuming here that you cut the joint by hand.)

I started wondering about tolerances when I started trying to face
joint wood. If I aimed for "perfect", meaning that I couldn't detect
any deviation from my Starrett, then I'd still be jointing. And I
concluded that seeking that level of accuracy doesn't make sense
because of the changeable nature of wood. (I plane the other side and
it bends 0.1" anyway.) So if perfect isn't the goal...then what is?
I picked 0.004", but I don't know if that's the right answer.