I am interested in keeping the best audio possible for my movie collection when I rip them for my HTPC. I am aware at the moment that there are no perfect ways to take the digital high def audio and output it to an amp because of the lack of HDMI 1.3, but I don't imagine it to stay that way forever.

So my question is, what are the best ways to take the HD Audio (dolby truehd or dts hd) and encode it into a format that will be playable when the hardware catches up, or even right away. I have read a bit about using FLAC to encode the audio as it will ensure lossless quality (which is ideal).

Any insights would be great!