If you work directly in the source repository that works actually really well on Github (if everybody works on its own fork instead, you're unfortunately out of luck). When opening a pull request, you just select the branch the pull request should be based on to be the previous branch in your stack. If one of those pull requests gets merged, Github will automatically rebase the stacked on onto the base branch. This way every pull requests contains exactly the changes you want it to contain, while you're still being able to stack changes by opening multiple pull requests, with each one being based on the branch of the previous one.
