Yea we've had some requests along these lines...I believe the first request was to be able to use DIFFzilla with Eclipse' backup history, but having the option to just replace the default diff tool with vsdiff.exe is something we would like to provide.
There is an open source external diff tool plug-in which supposedly allows you to replace the default Eclipse diff tool with whatever diff tool you want (
http://sourceforge.net/projects/externaldiff/). I'm not sure what versions of Eclipse it's compatible with, and how well it works, but you might want to try it out. If you do decide to try it, I would be interested in hearing how well it works

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- Ryan