Starting January 1st 2017, 00:00 UTC, movies submitted with FCEU will no longer be accepted. FCEU is not necessarily a horrible emulator, but it is simply out of date, with more modern emulators such as FCEUX, NESHawk and QuickNES all surpassing it in emulation accuracy and TAS tools.
Practically everyone already has moved on, of course (only three .fcm movies have been published in the past three years, one of which was an unrejection and another was originally created in 2008), which makes it safe to say that it is not popular as a TAS platform anymore and could be dropped more or less safely.
Note that FCEUX also supports importing .fcm files with a good rate of compatibility, so those that still use FCEU may also consider converting their movie over to FCEUX and submitting their movie as a .fm2 instead.
In case anyone has a run in progress and still wants to submit a .fcm movie after the date, you can post in this thread to request a
continuance. Continuances will be accepted until December 15th 2016, 23:59 UTC.
EDIT: Continuances are closed now.