One difference that is being implemented on some new 3D-enabled Blu-ray Disc Players is that addition of a second HDMI output; which provides one HDMI output for video and one for audio.
The reason for the addition of a second HDMI output is that 3D-enabled Blu-ray Disc players utilize HDMI 1.4 outputs. However, since "older" HDMI-equipped home theater receivers in current use are not HDMI 1.4 compliant, they are not able to pass an encoded 3D video signal that has to utilize the HDMI 1.4 connection. Note: If you are purchasing a new Home Theater Receiver, there are a growing number that are now HDMI 1.4 compliant.
So, to prevent any conflicts, a 3D-enabled Blu-ray Disc player with one HDMI 1.4 output for connection to a 3D-enabled TV for 3D access and an HDMI 1.3 output to connect to your home theater receiver can carry all of the audio that many HDMI-equipped home theater receivers need to access.
Ideally, if you really want to be fully 3D signal compliant across the entire connection chain of your home theater system, you need to have a receiver that is 3D compliant by having HDMI 1.4a connections), especially if you rely on your home theater receiver for video switching or processing.
However, you can avoid this additional costly upgrade by planning ahead. Find out three ways you can still use a non-3D compliant home theater receiver with a 3D TV and 3D Blu-ray Disc player.
In the grand scheme of things, upgrading to an HDMI 1.4 compliant home theater receiver, would be a low priority, as you can send the video signal directly from the Blu-ray Disc Player to the TV and the audio from the player to the home theater receiver separately, but it does add an extra cable connection to your setup, and you may not be able to access all of the available surround sound formats.