Qubes doesn't use video acceleration as it is less secure.
Mplayer is IMO the best option for video playback in VMs, as it focuses a lot
on optimizing without using acceleration.
You can also sacrifice some quality for speed with some of these options:
mplayer -vfm ffmpeg -sws 4 -lavdopts
skiploopfilter=all:fast:gray:lowres=3:threads=
You can change the default configuration and/or create an alias in either the
template or the dvm/appvm.
I set dropping frames(g key) to enabled, but change to hard(pressing g again)
if audio video timing is especially important.
You can also check if assigning more memory and vcpus helps, if you have not
already.
Launching many qubes, like qubes updater does, can also cause signifigant
stutter with slow drives in my experience.
Also remember that h264 decodes a lot faster.
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