DVD to MKV with multiple audio tracks and subtitles

Use MKVMergeGUI.

mkvmerge and mkvmerge GUI (or just mmg) are two programs created by Moritz Bunkus. They're part of the mkvtoolnix package. mkvmerge can read a lot of different multimedia files and put their contents into Matroska files. Unfortunately this is a command line program, and not everyone is comfortable working on the command line. This is where mkvmerge GUI comes into play. It is a GUI that provides the user with an intuitive but powerful interface to mkvmerge.

Try this example (source):

mkvmerge -o out.mkv input.avi input.srt

Save the following as something like DelMKVSubs.bat in the same directory mkvmerge.exe is in, edit the rootfolder variable as per your requirements and run the batch file:

@echo off
cls
set rootfolder=C:\
echo Enumerating all MKVs under %rootfolder%
echo.
for /r %rootfolder% %%a in (*.mkv) do (
    for /f %%b in ('mkvmerge -i "%%a" ^| find /c /i "subtitles"') do (
        if [%%b]==[0] (
            echo "%%a" has no subtitles
        ) else (
            echo.
            echo "%%a" has subtitles
            mkvmerge -q -o "%%~dpna (No Subs)%%~xa" -S "%%a"
            if errorlevel 1 (
                echo Warnings/errors generated during remuxing, original file not deleted
            ) else (
                del /f "%%a"
                echo Successfully remuxed to "%%~dpna (No Subs)%%~xa", original file deleted
            )
            echo.
        )
    )
)

The batch file should be easy enough to understand, but here's an overview nevertheless:

1. It uses for /r to recursively search %rootfolder% for all MKVs

2. It then runs mkvmerge -i on each MKV to check whether a subtitle track exists

3. If the MKV does contain subtitle tracks, it runs mkvmerge -S to remux the file while skipping all such tracks

4. Finally it checks the exit code of mkvmerge and if this (i.e. errorlevel) is 0 indicating success with no warnings/errors, it deletes the original file

For more see the mkvmerge documentation and also for /?, if /? etc. at the command prompt.