If you have a N3DS/N3DS XL, you can use the plex media player through the 3DS internet browser, if on your home computer you host 3D videos on the plex media server, you can choose to watch those films in 3D. I would know, I've used it before, currently I've only tried it with the 3D version of Guardians of the Galaxy, but I can confirm it does work.
Which does lead me to ultimately believe that if someone knew what they were doing, a 3DS homebrew media player could be developed that would be able to play 3D movies you own in a digital format. However, as always, easier said than done. Until then, I recommend Plex if you want to watch your movies in 3D on your 3DS. Its not a super simple setup though, I did have to use an online tutorial somewhere to get everything working properly, but once you do, you're golden.