Not having seen much past S3, I would have to say that I really like the 4-story S1 arc that starts with "There for the Grace of God" and ends with "The Serpent's Lair". Those eps- more than any of them- got me hooked on the show. My other favorite story arc was "Nemesis"/"Small Victories" that introduced the Replicators as another galactic menace to be reckoned with. The episode where they capture Apophis and he "dies" (Serpent Song) was really good too, as was most of S2. Darn. Now I'm going to have to start watching this show again. Thankfully, they have it all on Netflix!