WITHOUT A DOUBT, THE BEST EPISODE OF ATLANTIS, EVER
Ok, maybe that's pushing it a tad, but it would certainly be in my top 5. OUTSTANDING episode, that had me hooked the whole way through. Now I know why we had to sit through crapfests in recent weeks... so that they could pay for First Contact!
I love a good old fashioned Ancient puzzle, so really liked the light bulb bit.
Janus' lab activating... nice!
The extreme close up of the Daedalus exiting hyperspace
Hyperspace window opening at sea level

The new aliens were great, even though I stupidly watched that spoiler clip that showed who they really were. It's so nice to see some technologically advanced aliens for once, not just the same old Wraith storylines, or primative village of the week, every episode. The alien personal shield was one of the coolest effects Atlantis has ever done.
Very nice seeing Daniel back, although he's still too "cool", I think he was a lot more effective when he was slightly geekier, but that's just personal preference.
The bit with the Wraith ships exploding was awesome, as was Todd's reaction. That guy is a fantastic addition to the series.
Oh and the Stargate exploding scene at the end was one of the coolest dramatic scenes in the whole series. Wonderfully cool and exciting, and the cliffhanger was AAAAAARRRRRRRGGGGGGHHHHH in a

way. Nice final shot, though the editing could have been better.
Can't wait for part 2. I hope it's as good and exciting.