Well, it's not the best solution, but it's possibly the easiest. If you start the merge in Git (but before you act on it) Git will create a .BASE, .LOCAL and .REMOTE file in the same location as the file you need to merge.
In the case I've outlined above either .LOCAL or .REMOTE will be missing (depending on who deleted the file), but you can still go to the folder in question and manually diff either .BASE -> .REMOTE or .BASE -> .LOCAL.
This is probably easiest for Windows users.
If you really want to use the command line you can run
git merge-base <mergingBranch> HEAD
to find out the base commit hash. Then, using part of bundacia's answer above:
git difftool <mergeBase>..MERGE_HEAD -- foo.file