I don't own the series on Blu-Ray (The DVDs will suffice), but this review
suggest the picture is -- for the most part -- excellent in HD. There seem to be some minor problems related to visual effects (some were not rendered in HD), but they're a minor blemish.
It certainly won't have the problems of the Farscape
Blu-Rays, since unlike that series (which was upconverted from PAL, I believe), Stargate Atlantis
had HD masters.