Currently my favorite backup tool for my needs is rsnapshot. The only downside is the space wasted if files are just relocated. I have seen a similar question at severfault, but the author tried to implement his own solution.
In the past I used Legatos Networker and this problem was not an issue. However I am looking a cheaper alternative for my home files.
I am out of touch of all the backup tools available. Therefore I am not sure which opensource tools solve already the relocated files problem. Ideally it should be rsync based. I do not like Unison since it is not that great to keep different versions of my data.