A single branch of another repository can be easily placed under a subdirectory retaining its history. For example:
git subtree add --prefix=rails git://github.com/rails/rails.git master
This will appear as a single commit where all files of Rails master branch are added into "rails" directory. However the commit's title contains a reference to the old history tree:
Add 'rails/' from commit
<rev>
Where <rev> is a SHA-1 commit hash. You can still see the history, blame some changes.
git log <rev>
git blame <rev> -- README.md
Note that you can't see the directory prefix from here since this is an actual old branch left intact. You should treat this like a usual file move commit: you will need an extra jump when reaching it.
# finishes with all files added at once commit
git log rails/README.md
# then continue from original tree
git log <rev> -- README.md
There are more complex solutions like doing this manually or rewriting the history as described in other answers.
The git-subtree command is a part of official git-contrib, some packet managers install it by default (OS X Homebrew). But you might have to install it by yourself in addition to git.