It seems that Google has finally decided to ditch Flash which means that embedded Youtube videos no longer work on FFTogether. There's some fixing to be done, Bram.

You can listen to this beautiful compilation while doing it:
Or maybe not if you're a Chrome user.

I googled this a bit. It seems to be a simple matter of replacing some of the generated HTML code. This is what is currently generated:
<embed src="http://www.youtube.com/v/QaAcrSYlfvs&rel=1&fs=1" type="application/x-shockwave-flash" allowFullScreen="true" allowScriptAccess="never" wmode="transparent" width="425px" height="350px">
<noembed>
<a href="http://www.youtube.com/watch?v=QaAcrSYlfvs" target="_blank">http://www.youtube.com/watch?v=QaAcrSYlfvs</a>
</noembed>
</embed>
This should be the correct HTML:
<iframe width="425" height="350" src="https://www.youtube.com/embed/QaAcrSYlfvs" frameborder="0" allowfullscreen></iframe>
Widescreen support would also be nice.