This is Cloverfield (2008, Paramount & Bad Robot) with hardcoded Rifftrax commentary by Mike Nelson, Kevin Murphy, and Bill Corbett of MST3K fame.

The video is taken from FXG's release, e.g. cloverfield[2008]DvDrip[Eng]-FXG.avi.  The audio was created using VirtualDub and MixMeister; VirtualDub to save a .wav from the source and to replace the source audio, MixMeister Studio to synch the film's audio with the Rifftrax audio.  

Instructions:

MixMeister needs to be tweaked a bit to get this to work, I did it by selecting No Transition for both tracks & deleting all Measure Markers, cropping the Rifftrax audio, and then aligning the tracks.  It is also essential to make the movie audio Track 1 and Rifftrax audio Track 2 if you do it this way.  Then Export the MixMeister playlist as a single .wav file.  Finally, replace the source audio with VirtualDub by loading up the original video and selecting options Video -> Direct Stream Copy & Audio -> WAV Audio (& choosing your Rifftraxed wav file, wherever you saved it) and Save as Avi.


VirtualDub: 
http://www.virtualdub.org/

MixMeister Studio: 
http://www.mixmeister.com/

Please donate to Rifftrax to keep these commentaries coming! 
http://www.rifftrax.com/donate