Webm video works fine for me. Make sure your ffmpeg is compiled to support webm

ffmpegthumbnailer -i test.webm -o test.png
outputs

"Not a native file, thumbnailing will likely fail"

Same with this:
ffmpegthumbnailer -i test.mp4 -o test.png
"Not a native file, thumbnailing will likely fail"

But MP4 is working in PCManFM and WebM is not. Am I using the right command 
line arguments? Or am I missing libraries? (libvpx 1.3.0 is installed)

WebM VP8 support (ffmpeg -codecs):
Decoding supported, Encoding supported, Video codec, Lossy compression

FFmpeg logs:
Codec support (ffmpeg -codecs): http://pastebin.com/HTPrheMS
Buildconfig (ffmpeg -buildconfig): http://pastebin.com/VmZzbwPf
ffprobe test.webm:
Input #0, matroska,webm, from 'test.webm':
  Metadata:
    encoder         : google
  Duration: 00:05:34.99, start: 0.000000, bitrate: 893 kb/s
    Stream #0:0(eng): Video: vp8, yuv420p, 640x360, SAR 1:1 DAR 16:9, 1k fps, 29.92 tbr, 1k tbn, 1k tbc (default)
    Stream #0:1: Audio: vorbis, 44100 Hz, stereo, fltp (default)

Can you provide me a link to a file that doesn't work?

And please try with the latest version: 2.0.9

The command from webm to png worked (using 2.0.8), but I didn't check the 
resulting png file at first because of the warning (I needed to press F5 to 
refresh, forgot to do that).

So thumbnailing both files worked. I installed PCManFM from git to no avail. I 
still wonder why it's not working. Do you think upgrading to ffmpegthumbnailer 
2.0.9 will resolve the issue?

The warning you get is related to the gio path handling. Something was fixed 
there in the latest release.

Hi again. I'm trying to compile 2.0.9, but the ./configure says at the end:

CONFIGURATION SUMMARY ----
png support          : disabled
jpeg support         : disabled
gio support          : disabled
register thumbnailer : disabled
unittests            : disabled
debug mode           : disabled

How can I enable GIO support?

Version 2.0.8 on Mint has the same issue as Manjaro Linux with Thunar (this 
time with Nemo, the forked Nautilus) being: MP4 works, WebM doesn't.

use ./configure --enable-gio

You als need to install libpng-dev or libjpeg-dev

The first three options are now "enabled". Make doesn't work, what's wrong here?
http://pastebin.com/WkYJ5dKu (I just entered make at cli)

Latest ffmpegthumbnailer requires a more recent version of ffmpeg

I have been able to compile ffmpegthumbnailer 2.0.9 on Manjaro Linux with 
ffmpeg 2.2.4, with GIO support, PNG support and JPEG support. The warning is 
fixed but the original problem still persists: WebM thumbnails are not 
displayed in PCManFM neither Thunar.

If ffmpegthumbnailer works from the command line you probably didn't configure 
the thumbnailer correctly to work with your file browser.

As suggested by PCMan (see [1]), adding video/webm to
https://code.google.com/p/ffmpegthumbnailer/source/browse/trunk/dist/ffmpegthumb
nailer.thumbnailer (which is located in 
/usr/share/thumbnailers/ffmpegthumbnailer.thumbnailer) solves the issue: WebM 
thumbnailing now works in both PCManFM and Thunar with ffmpegthumbnailer 2.0.9.

Could you add video/webm to the ffmpegthumbnailer.thumbnailer source file? 
Thanks!

[1] http://sourceforge.net/p/pcmanfm/feature-requests/341/

webm has been added to the thumbnailer file

[deleted comment]

Just add "video/webm;" to the end of 
/usr/share/thumbnailers/ffmpegthumbnailer.thumbnailer