Sakugabooru's MP4 encoder.
Here is a Windows-only tool of mine that will help encoding MP4 files to be uploaded to Sakugabooru. It is user-friendly and does all the job at once.

I went with MP4 instead of WebM because the MP4 encoding is faster and achieves a better quality/size ratio.

Please refer to the readme file to look for the instructions and for any technical information.

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Download: https://mega.nz/#!elp23ISb!j2s6ajL2clI2UT-uHTdJ83fciTVqXtS_pR0jhXiZpGs

EDIT: Someone messaged me to bring a bug occuring with 480px-high input files to my attention. So here is an updated version (with minor optimizations).
Sorry for bugging you, but I'm getting this error here:

Invalid duration specification for ss: 00:00:00:00
tobanga said:
Sorry for bugging you, but I'm getting this error here:

Invalid duration specification for ss: 00:00:00:00
You entered 00:00:00:00 ?

If so, I think that's not the correct format.
If you want to do milliseconds, separate it with a period.
You could just enter 0 in this case. You don't need to explicitly enter every leading zero or trailing post-decimal 0.