I just bought this season a few days ago and having finally seen it, I can say that it's awesome! Although I liked every episode without Lucius Lavin, my favorite episode of the season is "Prodigy" because of all the sweet special effects. As I said though, it was a great season. Here's an annoyingly in depth list of the other episodes that rank among my favorite.
"McKay and Mrs. Miller" - Who can forget about Meredith?
"The Return" (both parts) - When you mix the Atlantis cast with Jack O'Neill, Richard Woolsey, a couple hundred Ancients, and a group of robots who like to stick their hands in people's heads, you're bound to come up with something good! Okay, maybe not, but it turned out great.
"Echoes" - QUOTE ...the Canadian Football League is a joke...Meredith. UNQUOTE
"Tao of Rodney" - McKay swiped a donut, read people's minds, invented a new math, and even made the lights flicker!
"Sunday" - I feel so mad everytime I see Beckett make the hand-off! Why him?!
"Vengeance" - I don't care if this was a rip-off of the average monster movie, I liked it.
"First Strike" - Again, great special effects...and references to Marvel comic books.