Almost every media player now can play back 3D MKV files.
The difference with the Popcorn Hour is that it supports the official Matroska standard for properly making one without going through a lot of caveats like manually switching the 3D display to right mode (2D, 3D SBS, 3D TAB).
This means if you have a 3D MKV file, the media player will send the proper signaling via HDMI across the chain to tell the 3D display to switch to the proper mode (Side by side or Top and Bottom). This doesn't need HDMI 1.4
There is currently no media player that can handle true 3d bluray backups. This requires the player to be able to decode 2 x 1080p streams (also called 4k resolution). The current set of media players can only output 2 x 720p streams + HD Audio.
If you require HD Audio capability, you will also need an AVR that supports "3D HDMI Passthrough mode" without it, you're limited to just playing back standard Dolby & DTS audio tracks within the movie.