This articles comes from a post by Darkmantis, reformatted with minor modifications.
It's free, and a great way to re-encode your mkv, 264 files into an AVI container containing a Mpeg4 stream with Mp3 audio.
Of course, you can change any aspect of the video, audio type, video size, etc.
I have tried over 20 programs and this is obviously the best program out there, plus it's FREE. No gimicks, just pure and simply freeware. I have been trying to get the word out to everyone about this and I stumbled upon this by chance.
Usage to make a high quality MP4 Edit
At the top left corner it will say, "Select the Output container"
At this prompt you will select the container type for your media file. A container is like a bottle - it holds liquid and the liquid is your stream (just in case anyone else doesn't know what a container stands for).
The middle prompt will say "Select Output Codec"
At this prompt select "Mpeg-4" . I choose mpeg 4 because it's the highest quality codec that I can use on the Iomega Drive that is the closest, in my opinion, to the H264 or MKV file. Of course, you can select divx, mpeg-2 or whatever you feel like.
On the far right at the top of the screen you will see:
Select the output audio codec
At this prompt you can select your codec to carry your audio. The most popular one is probably Ac3 and Mp3. I had problems in the past with converting MKV files, mainly with the audio sounding screwed up while the picture was perfect. So for now, select "MP3".
Below that is your Video Stream Options.
I don't check any of the first options, only under video scale, I choose "NoChange". Most of the videos that I convert are already in 16:9 format, so I don't mess with the original size. But, if you need to, you can correct the size of your video file here by changing the numbers.
I also leave Aspect alone and on the Frame/sec section, I choose "29.97" or 30 fps. I usually leave it at 29.97 - most video files are rendered atleast with 25 or 29.97. Obviously the higher the number, the smoother the video will seem to be. But 29.97 is the best for most videos. You will probably want to check the frame rate of the original video and use the same figure. Instructions for checking the frame rate are further down.
Bitrate KBPS: The higher the number, the higher the quality will be with your video, but the larger the file. The lower the number, the more blocky it will become but it will compress better.
Select 9600 for a good, high quality picture.
Under your video options, check "Hi Quality" and 48k Audio.
Next, click on Other Opts under those options in the video options area where you just clicked Hi Quality. You will see a box appear on the lower left side and you can make more adjustments here, but I chose to "Hide Subtitles"
Press the Other Opts button again to make that new window dissappear.
I check the 48000 audio, 2 channels and 96 bitrate kbps. Dvd language track is default.
Now, where it says "drop multimedia file here" - you can open your folder to your videos and drag and drop a video in there, or if you have multiple (or single) video files, you can right click and open the files instead.
Once your video is in the list, you can double click on the video to see the current encoding details, such as frame rate and bit rate.
I don't change any of the normal settings if you right click on an open area to get the other options that aren't on that screen. The only thing that I changed was a file location for my desktop to save the videos post conversion.
Press the Encode (Active Files) button to begin the conversion process. It will batch encode each one.