Hi,

I would like to render a project, with the same quality & codecs as original into matroska continer (mkv).

I have a file from Nikon D90.

Input #0, avi, from 'DSC_0076.AVI':
Metadata:
maker : NIKON CORPORATION
model : NIKON D90
creation_time : 2011-07-21 18:42:27
Duration: 00:02:06.99, start: 0.000000, bitrate: 21865 kb/s
Stream #0.0: Video: mjpeg, yuvj422p, 1280x720, 24 tbr, 24 tbn, 24 tbc
Stream #0.1: Audio: pcm_s16le, 11025 Hz, 1 channels, s16, 176 kb/s

So I have made customize profile for rendering with options:
vcodec=mjpeg pix_fmt=yuvj422p acodec=pcm_s16le tbn=24 tbr=24 tbc=24

As a result I have a file with paramets:
[matroska,webm @ 0x7fbe90] Estimating duration from bitrate, this may be inaccurate
Input #0, matroska,webm, from 'untitled3.mkv':
Metadata:
ENCODER : Lavf52.110.0
Duration: 00:02:07.00, start: 0.000000, bitrate: N/A
Stream #0.0: Video: mjpeg, yuvj422p, 1280x720 [PAR 1:1 DAR 16:9], 24 fps, 24 tbr, 1k tbn, 24 tbc (default)
Stream #0.1: Audio: pcm_s16le, 48000 Hz, 2 channels, s16, 1536 kb/s (default)


On the paper it looks the same, but quality of video is very poor.
What should I add to my custom rendering profile?

You need to experiment with qscale= and b= options to see what FFmpeg supports for setting the quality level of MJPEG. I do not recall at the moment.