This is a known problem with Github. If you search on http://google.com
you will find a lot of discussions about this. It seams they are aware of this and hopefully they will make better support in the future.
I usually do each pull request from the master branch. On the ones that depend on another pull request I write in the comments that this depend on #XXXX. The test cases will fail on the pull requests (if test cases are included) but this is ok. When the first pull request in merged into master we can just rerun the tests on the next pull request. We continue like that until all are merged.
This is not a perfect solution but it usually work pretty well.
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