Okay, I wish someone would've told me about this before I started ripping all my movies for easier access... and I'm sure there are plenty of ways of doing selectable audio and subtitles, but this way works for me.

One of the biggest problems I had was that I missed the audio commentaries. Once in a long while, I do break open an old DVD and put on the commentary while I write articles, but it's not very often. So below is a step-by-step guide on how to rip your movie for your iPad, Apple TV, WD-TV, and PS3. I'm leaving Xbox out because Xbox does not support "complex" audio and won't play MP4 files since they updated their dashboard.

If you have an unprotected DVD or Bluray, you can just skip to #3: Handbrake.

#1: Rip your movie
I have a lifetime license for DVDfab.com, so it's the software I use. It is expensive, but I think it's worth it. You might already have similar ripping software, just make sure your software can rip movies with multiple audio and extract subtitles. For DVDFab, what you need to do is rip it in MKV remux, capturing the multiple audio and "extracting IDX" (subtitles) in your options. Generally, I would rip the main audio and the commentary and the English subtitles (if available).

#2: Convert SUB to SRT
Because the subtitles are stored as images, you need to convert the images to text. I use a free software called SubtitleEdit. For images it doesn't understand, it will ask your input. It's not perfect, but it is free. The optical recognition software has a hard time understanding "I" and "1" and often mixes the two. When you're done, save it as a SRT file (this is a text file).

#3: Handbrake
The latest Handbrake is pre-set for the best quality, so you don't really need to muck around too much, unless you want to downgrade your video. What I would recommend is to scale the video to 720p or less because of streaming issues (anything larger will take a long time to buffer). Under audio, select "add all audio" and under subtitles, click on "import" and add your SRT file. Do not select "forced" (this is only applies to forced dialogue). Select "burn" and "default".

3.5: Hardcoding (alternative option)
Step #3 is for Closed Caption (Apple devices can turn on and off the CC as Subtitles), if you prefer to Hardcode the subtitles you can use the free Any Video Converter. You just need to have the same name as SRT with your MKV file. NOTE: Hardcoding is permanent; you cannot remove the subtitles.

#4: Tag your file
You don't really need this step, but if you're already going through all these processes, you might as well make it pretty. There is plenty of tagging software, use the one you like. I recommend MetaX, which was originally free but now costs $10. I believe it's still free on Mac OS.

Congratulations, you now have a x264 movie file that will play on most devices, including your iPad and PS3. The PlayStation 3 does not have the ability to view Closed Caption, however, you can always switch to the English audio track. If your player knows how to read SRT files, then just include the SRT file, along with your movie file and you're golden.

I know it's a lot of work. Most people have stopped at step #1, or they are more than happy to fork over $15-20 to "own" a digital copy. I reckon if I already own the disc, I'm not going to pay for the same movie again. I hope this guide helps you out. I had to go through a lot of mistakes to get here.

Here's the files, as seen on my iPad.  Note: subtitles can be turned off. I'll probably update the cover artwork with a high res version, not happy how it looked.