I run native and have 3 resolutions checked off (480p, 720p, 1080i) because those are the ONLY resolutions supported by my earlier generation Samsung Plasma over HDMI.
My TV itself is only 720p model from a few years ago when 1080p required an extra $1000. It still looks better with Native. The TV does a good job at converting the picture to the native panel resolution.
When comparing DirecTV HD to cable HD on ClearQAM tuner, they are pretty close, but local affiliates like ABC,NBC,CBS,PBS,FOX look a little sharper on the Cable signal. The cable company encrypts national HD channels, so I can't really compare something like Discovery or ESPN for example. I do have to say that those national channels on DirecTV look crystal clear, even when sitting close to the screen. The only nationals that are "in the clear" on the cable wire are QVC HD, CSPAN1 & 2 HD. DirecTV doesn't have these in HD to compare, but the cable side looks pretty good, and the QVC one has 3 channels on that same frequency. That's not a hard channel to encode though because it's pretty much static text and very slow camera panning on whatever their selling.
So my verdict?
DirecTV HD Nationals are crystal clear and pristine. Better than any thing else out there.
DirecTV local HD channels tend to take a softer look, but don't get me wrong, it still looks crystal clear and you need a real good eye to see the difference. I think the MPEG2 to MPEG4 conversion looses a bit of detail for the locals, but it's not bothersome.
Another thing to check, see if your TV has 1:1 pixel mapping, or a no overscan mode. My TV calls it "Just Scan", and to me I think it looks best in this mode, as no detail is lost off the screen.