Right click on a source managed file > select TortoiseSVN > Settings > drill down to External Programs > Diff Viewer > click External for "Configure the program used for comparing different revisions of files" and enter the path
C:\Program Files (x86)\WinMerge\WinMergeU.exe -e -s -x -ub -dl %bname -dr %yname %base %mine.
Note 1. Make sure the path to WinMergeU.exe is correct!
Note 2. I have been using this for ages already, but the "-s" argument is a neat recent addition for me - to force WinMerge to use just a single instance.