Wow, I absolutely LOVED this episode.
I don't watch CSI (not enough spaceships in it) so I didn't get the specific homages, but I figured they were something along those lines. And I really didn't need to know CSI to enjoy the extra elements of this episode.
It didn't take long for me to stop watching it with an eye towards figuring out the angle ("is this a broken timeline? An alternate reality? A hallucination?") and just got sucked into this totally different take on the show. Learning why everything was different was just icing on the cake.
Looks like Atlantis is going out in style.