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One problem with the Shuttle cases is the lack of slots. The Shuttle cases I have looked at have 1-AGP slot and 1-PCI slot. That means you are done once you add a video card plus a tuner card such as the Hauppauge PVR-250. To me this is a huge downside to these cases. You couldn't add a second tuner or a different sound card or whatever.
I just got a new PC - a 3.2GHz CPU in an Antec Sonata case with a Asus P4P-800DLX mobo. The CPU comes with its own fan which is too noisy for my liking. I will likely be replacing this fan with a quieter Zalman fan/heatsink combo. This is something to keep in mind if you get a 3.0GHz or faster system which I assume you will.
I don't know what CPUs the Shuttle can accept, but you will likely not be able to put one of these larger heatsinks into it so you may be stuck with a noisy fan if you want one of the faster processors.
If you are putting together such a high end HTPC then why only use s-video? HDTV looks AMAZING and if cost is not an issue upgrade your TV to an HDTV. If size isn't an issue then rear projection HTPCs can be had for a reasonable price. Then you should get a much better picture out of component or DVI or RGB or whatever your TV accepts.
If you're serving video to other locations you might want to get a media player like the Gateway Connected DVD player for those locations. Then you can stream MPEG or DivX files over your LAN either wired or wireless. The Gateway player is < $200.
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