In Git one can specify these in .gitattributes and perform some additional configuration:
git config diff.difftool.command ...
git config merge.mergetool.driver ...
In Mercurial it is possible to specify patterns in hgrc file ([diff-patterns] and [merge-patterns] sections).
How to achieve this in Subversion?
The red-book for Subversion (normally the source of all knowledge) is not too specific here. It names that there is the option to configure diff-cmd and diff3-cmd and that it is possible to add extensions to the call.
However, it states the following:
The decision on when to fire off a contextual two- or three-way diff as part of a larger Subversion operation is made entirely by Subversion and is affected by, among other things, whether the files being operated on are human-readable as determined by their svn:mime-type property. This means, for example, that even if you had the niftiest Microsoft Word-aware differencing or merging tool in the universe, it would never be invoked by Subversion as long as your versioned Word documents had a configured MIME type that denoted that they were not human-readable (such as application/msword).
It does not say how to influence that decision :-(
If you are using the tool TortoiseSVN, there are configuration options included to specify the used diff tool per mime-type of the file under consideration. The path to that configuration is: TortoiseSVN > Settings > External Programs > Diff Viewer > Advanced.... Perhaps that is an option for you.
My personal opinion here is that the subversion team thinks that you should use a wrapper as diff-tool anyway, and to do there the decision what tool to use with which specific configuration based on the mime-type.
