google probably already told you, you could buy a couple proprietary software who could do that, but just in case : videocompare, tmpgenc, vidlord...
This one's free : http://forum.doom9.org/showthread.php?t=138430
(working download links at the end of the thread)
Untested because my wine setup is completely screwed right now. It doesn't do side by side but stacked playback (unless you have a very good lcd you won't be seeing the same thing by playing the same vid in two opposite corners of the screen anyway)
If you think you really need side by side you can use avisynth to do what zimmer said.
clip1 = DirectShowSource("C:\MyEncode1.foo", audio=false)
clip2 = DirectShowSource("C:\MyEncode2.foo", audio=false)
You don't need to do an encode (wich would add its own encoding artifacts anyway), just make a project that would produce an encode of the two vids playing together and skip through the file.