This is what I did to get 3D MKVs playing on my EVO 3D.
What you need:
- Any Side-By-Side 3D MKV (or any other Video container actually, as long as it's SBS 3D)
- Freemake (get it here)
Step 1: Open Freemake and click
File >
Add Video... Browse to your video file.
Step 2: Click
to Android...
Step 3: Click
Add your preset...
Step 4: Choose the following settings:
Title - qHD
Width - 960
Height - 540
Channels - Stereo
Sample rate - Original
(make your screen look like mine)
Click
OK
Step 5: Browse to the location where you want to save your movie.
Click
Convert
Step 6: Your video is converting
Step 7: Your video is finished converting.
Step 8: Copy your video to your MicroSD card. Safely remove the drive and disconnect your phone from your computer.
Step 9: Browse to the movie in Gallery. Click
menu on the android and choose
Play in 3d. Click
OK on the Side-By-Side warning.
Enjoy!
Note 1: I'm open to suggestions on improving this guide so please, let me know.
Note 2: Pictures uploaded.

Note 3: Changed from hand brake to Freemake since handbrake was producing videos with no audio for both myself and another user that PM'd me.