I have an MKV that has three different subtitles in three different languages embedded within the MKV itself. I can switch between them using the subtitle option in VLC. There is no separate SRT file that goes with this. Nor is it hardsubed or burned into the screen.

My player keeps defaulting to another language. How do I change the subtitle to the one I want to use?

On the player by pressing the "Subtitle" button and it should show you the options and select the right one.

If you want to clean up the file so that only the subs that you want are contained, use the MKVMerge function of MKVToolnix.

It's a 2 minute job once you learn how to do it.

Hey, thanks. How do I do that?

I'm a noob to all this so I don't know.

Download MKVToolnix from the Internet (FREE). Google is your friend.

Run the "MKVmerge" component and open your MKV file with it.
Tick what streams you want to keep
Remux to new file.

Easy peasy. Give it a go.

Hey thanks. I never knew about this tool.

It was a little difficult figuring out which subtitle to keep and which ones to delete since they were only labeled "subtitle" and there were four of them, but I did it by trial & error.

Again, thanks!

Subtitle Edit will actually allow you to inspect them in the file.

MKVToolnix is a great FREE tool. Use it all the time!!!!

Yea it does what you say.

Does it work on mp4 files as well?

Don't know as I refuse to use MP4 crap.

Don't like mp4s?

Why's that?

I've been impressed with their small file size while keeping a high quality picture, something that I never had with AVIs

MP4 is only a container, just like AVI or MKV. The size of the files comes from the codecs used for audio and video and their settings (bitrate). So you can get the same file size from remuxing an MP4 file to MKV and MKVToolnix can actually do this. The issue you describe with AVI files stems from using older codecs such as DivX/XVid or MPEG2 instead of newer MPEG4 based codecs (H264). The newer codecs give better quality with lower bitrates.