I use MakeMKV to put the video files into the MKV container. While doing this I only select the audio option I want to keep (DTS if it's available). Once I have the completed MKV file (5-7GB), I use Vidcoder, which is an enhanced GUI for Handbrake, to encode (compress) the file (1-2GB). Under the audio settings I choose Passthru (Auto), which keeps the audio in the exact same format as the original while still compressing the video. I chose to do this because I wanted the file compression but also wanted full quality audio. This may not be for everyone since I know a lot of products won't play DTS without transcoding, so it really depends on the playback device you are using. Since I only play them back on Boxee and my Samsung SMART TV, I leave the full audio in the file.
Router: ASUS rt-n56u (Black Diamond)
Server: Intel Quad Core 8200, Radeon 3450, 4GB RAM, Windows 7 Ultimate, Wired Gigabit
Boxee Box: latest firmware, Wired Ethernet
Connectivity: Netgear AV500 Powerline Adapters