I've had that problem for some time now, since I bought an Aspen Les Paul-style guitar from the 70's, all of the strings have a sharp intonation, and not matter what I do, it won't change, and even the local guitar shop couldn't fix it.
But don't trash it! Try these four simple steps to make it at least 75% less noticeable (hopefully).
Sorry about the terrible picture quality; I am poor.
What you'll need:
* Guitar with bad intonation issues
*Something to tune by (a tuner, a guitar, etc., etc.)
Step 1: Step One
Locate your capo.
Step 2: Step Two
Step 3: Step 3
Step 4: Step Four
Now, this doesn't really fix the problem, just helps to mask it (it's still there but it is much, much harder for me to notice it while playing it like this).
Results may vary, but this worked for me. Maybe someone else will get use from it.
*And also, because I'm pretty sure everybody is tire of hearing it, I put this at the end*
First Instructable. Like it or hate it or love it or be completely indifferent. And whatever your decision is, I'll let you pretend that you made the decision all by yourself, and that it wasn't actually me making you feel the way the way you do.