Building a NAS/Server and two HTPCs is a good idea. Preferably, you don't want to transcode anything. Your HTPCs should be built with the idea in mind that they can playback the full uncompressed blu-ray rips. You'll want a completely wired network (stay away from wireless except the for the hand-held devices.) And depending on what all they want to watch, your front-end software on the HTPCs needs to be tailored to what they wish to consume. If they want to watch TV on the HTPCs, then without a doubt, Windows Media Center is the first place to look. If movie playback and audio playback is all you need, then XBMC could work as well. Plex offers built in transcoding to devices such as tablets, phones, etc... if you really need to support these devices.
I'm assuming that you know "how" to build all of this, and are really just looking for advice on the architecture?