VideoProv Converter AI wins over Shutter Encoder
I tried Shutter Encoder because the reviews on the net that it was the best for converting MOV files to WEBM with Alpha. This was misinformation because very few files out of hundres was recognized by Unity 3D. However, VideoProc Converter AI worked 100% in converting our hundreds of files. I highly recommend this converter when numerous professional convertions are involved. This software has all the expert features that you would need such as converting from opus to vortis and tons more.