I was checking out prices on the 6550, along with P35 mobos and combos of the two. What I found was that it was sometimes cheaper to go with separates.
Now with the holiday season here, prices have fallen a noticeable amount on everything, which is good news.
For GPU, I would encourage something based on the HD2600 series, or an 8600. You won't want a furnace in your HTPC, so the 2900 and 8800 series are not a good idea unless you're trying to use the thing for power-gaming too. You could go with onboard, but you wouldn't get the improved video processing that you'll get with a GPU card. See past THG articles on these and the HQV test results for more info. I believe both ATi 2600 and NVidia 8600 series are available with no-fan, internal-fan and case-venting-fan configurations, so choose based on the ability of your case to vent the heat without assistance.
For CPU, it depends entirely on how much encoding / transcoding you plan to do. If you don't need high performance, then aim for low-power with a slower dual-core... again to control heat. I'm looking at 6550s, and even those are overkill for most HTPC tasks. Plus, you'll have plenty of headroom to upgrade when future prices come down.
For a Mobo with onboard RAID, consider RAID mobility. Intel's SB chips tend to at least offer some support for Mobo upgrading (e.g. from ICH7R to ICH9R, if a 7R-based mobo dies). THG had a recent article about this too. Worth considering if you don't want to have to restore from a backup in the event of a failure. Also consider support for future platforms, such as offered by the P35 chipset. Unless you're gaming with dual ATi cards, the X38 won't do much for you. And again for HTPC you want lower power, which appears to be Intel-based chipsets in the latest Mobo tests.
Are your tuners all PCI? If so, you'll need to pay attention to Mobo layouts and GPU choice because finding a Mobo with 3+ usable PCI slots while using a dual-slot GPU is becoming more complicated.