Basically, I'm looking for something like Windirstat that works well on the command line and is easy to distribute over a network.
I've tried sysinternals du (can't exclude/include file types), diruse (limited like du), cygwin du (too slow). I've also tried all the graphical tools I can find, and none have a command line interface.
Any hidden gem I'm missing?
I've found Xinorbis. It seems brilliant.
If you're willing/able to take Unix tools to your Windows machine (which I guess you are, since you're using du already), you could try using findutils from cygwin in a bash script:
NB - this is roughly what I'd do; it's not tested.
Surely, this could be done more efficiently if you would like to do this for every type of file in the system. For single types, it probably wouldn't get much better with dedicated tools since this should be so IO-bound.