Good Lord, 20 posts. My newest bike has internally routed cable but I haven't had to replace it. I didn't realize it was this hard. Maybe it is, maybe it isn't, but I have to think Park Tool or Sheldon Brown or some other technical authority has a best practice tutorial in one of the usual places. If I had to do it myself I would already be on it. Let's get this thread notched up to #useful status and find a peer reviewed authority to post a link from.
Edit:
A start? <shrug>