I wouldn't go Atom for a HTPC. People forget that watching videos isn't the only thing you do with an HTPC. It might be able to do 1080p in an ION configuration but I've read a lot of complaints about the UI being slow, antivirus slow, etc. If watching videos is all you want to do you might as well get one of those media boxes to stream stuff from a NAS. I just put together a HTPC with a Phenom II X3 705e and Gigabyte AM3 DDR3 785G mobo and it flies with Windows 7. Beyond my first hand experience I've read lots of good things about the Athlon II Regor chips for an HTPC and that Sempron 140 too.
Just think about what else you want to do besides watch videos.
Those i3/i5 Clarkdale CPUs are very interesting. I just ordered an i5-650 and over the next few months will piece together an HTPC with one of those. I am particularly interested in the encoding aspects of that CPU and the support for 7.1 bitstreaming (which the AMD 785G solution doesn't do w/o an add-in card). It'll be fun to compare the two side-by-side.