There is an awesome tool which is called hub, which provides useful tools to clean up pull requests and generally "helps you win at git".
One useful command in this context is:
git am -3 <url>
This allows you to grab the changes from a url and apply its commits/changes to your current local git without even fetching the remote repository (which comes in handy with large repositories).
If you use this command with the git webpage of the commit you want to grab, you end up with this commit in your git. Even more useful: the commit author is kept and not replaced by you (as it would if you use git rebase). If you push this to your repo, the changes will be committed by you, but authored by the original author.
A very good ressource on this topic is this guide by Nathaniel Talbott. It shows a great workflow to work with pull requests instead of relying on the "malicious" merge pull request button on github.