WinMerge

From http://winmerge.org/:
Installation

Just download the installer and double-click it.

Or you may simply unzip the binary zip package into the desired location, 
and run WinMergeU.exe (except for Windows 98/ME users who should use WinMerge.exe).

For more information, please see the Installation section of the Manual.

OK, let's look @ the manual...

From http://winmerge.org/2.4/manual/installing.html:
5.3. Installing from archive

WinMerge is pretty much independent from other system components. It doesn't 
integrate tightly to Windows or use lots of dlls. WinMerge[U].exe itself is 
dependent of MFC42[U].dll (and MSVCRT.dll) in addition to some system DLLs. 
So if mentioned DLLs already are installed to system, only WinMerge[U].exe 
is needed to run WinMerge.

Archive files have correct folder structure. WinMerge should be unzipped 
preserving folder structure to destination folder, for example C:\Program Files\. 
Root folder created has name /WinMerge-version, for example /WinMerge-2.4.0. This 
folder can be renamed or files copied to other folder (preserving folder structure!).

Seems to me if it is common/system dll files you might be alright.
Why don't you download it & try it out?

~Lurk~

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I used Portable RegShot to check, and the zip-based .exe (WinMergeU.exe) creates the following key: HKCU\Software\Thingamahoochie\WinMerge, along with 6 subkeys and 82 values. You'd need to make a launch wrapper to deal with them, for true portability.

I didn't find a setting to make it use a local .INI file. Perhaps someone would like to patch the source to do this? Or at least make a Feature Request at SF? I checked the SF trackers (ToDo, Bugs, etc) for any existing request (searched for portable and ini, individually) and found none.