I have been looking a simple way to convert my *.mkv TV series collections to *.mp4 so I can watch it on my TV. Luckily, I stumbled upon a post in stackoverflow about it. So I took the code and modified it a bit so it can automatically find all *.mkv files in a directory (recursively), convert them to *.mp4 and place it the same directory. The only dependency you need is avconv which can be installed easily on Debian/Ubuntu by sudo apt-get install libav-tools and you are ready to run the script:
#!/bin/sh
findpath=$1
: ${findpath:="."}
find "$findpath" -name '*.mkv' | while read f ; do
dir=$(dirname "$f");
file=$(basename "$f");
# ext="${filename##*.}";
name="${file%.*}";
# echo "avconv -i \"$f\" -codec copy \"$dir/$name.mp4\"";
avconv -i "$f" -codec copy "$dir/$name.mp4" </dev/null;
# rm -f "$f";
done