Today I stumbled upon a new Team Explorer extension for TFS in Visual Studio. It almost immediately
made it on my shortlist of things that I need to have on every Visual Studio installation. It's simple, but brilliant.
Ok, enough praise :).
This extension nests itself into Team Explorer and adds a Merge button there. Upon selection of the source and target branch it will automatically list all Change Sets that need merging and when you merge them it automatically associates the correct Change Sets and Work Items. The latter is exactly why I instantly fell in love.