Beyond Compare is probably the the best file (and folder) comparison I have come across. It can even compare zip files.
If you are tired of using the shitty compare tool that is a default in clearcase there is indeed a way to switch this to use beyond compare instead
1. Go into the "C:\Program Files\Rational\ClearCase\lib\mgrs" directory.
2. Create a backup of the file named "map".
3. Edit "map" and change the line:
text_file_delta xcompare ..\..\bin\cleardiffmrg.exe
text_file_delta xcompare C:\Progra~1\Beyond~1\bc2.exe
Thats it, next time you compare two versions of a file in the version tree or you compare with previous version, beyond compare will be used instead.
Alternately if you want to use winmerge (which is opensource and free) , then it gives you an option to replace the default viewer when you install it.