Currently, PortableApps offers WinMerge. Unfortunately, WinMerge has known bugs and hasn't really been updated in quite some time.
There is a popular fork of WinMerge, called WinMerge2011, that has received significant updates. It is open source, and so all updates can be viewed. I have nothing to do with the development... I'm just a user of that software.
To see some of the problems with the original WinMerge, try exporting your registry as a text file, then use your computer a little, and make another export. Try using original WinMerge to compare them. It will generate an error. (This is just a simple example that is easy to reproduce.) WinMerge2011 will handle this example without problems.
Can you switch the PortableApps WinMerge to WinMerge2011?
It is located at: https://bitbucket.org/jtuc/winmerge2011/downloads