This question is pretty old, but it still seems important, as it isn't easy to put relative references from readme.md to wiki pages on Github.
I played around a little bit and this relative link seems to work pretty well:
[Your wiki page](../../wiki/your-wiki-page)
The two ../
will remove /blob/master/
and use your base as a starting point. I haven't tried this on other repositories than Github, though (there may be compatibility issues).