S1: Thor's Hammer (featuring James Earl Jones) is fun, There But For the Grace of God and Within the Serpent's Grasp are obvious standouts.
S2: The Fifth Race is a defining moment in the series and one of the best early episodes.
S3: I like Seth and Foothold.
S4: Window of Opportunity is the obvious fan favorite. I like Chain Reaction for starting the Maybourne redemption arc.
S5: Enemies, Fail Safe, Revelations. Probably Enemies for me, but I need to rewatch Threshold.
S6: The Jonas season. Redemption, Part 2 is fun, as well as Prometheus, Paradise Lost, and Memento.
S7: Evolution, Part 1/2 are fun, and Lost City, Part 2 is epic.
S8: Reckoning, Part 2 for the epic conclusion, Moebius, Part 1/2 for the fun factor.
S9: The opening three-parter is pretty strong for what it has to do. I like Ethon for the demise of Prometheus, and Camelot for the Supergate battle.
S10: Unending is the safe pick, although I think the demise of the Asgard is plot contrivance and unsupported by biological science. The Shroud is good but a bit awkward. I'll go with The Quest Part 1/2.
If I have to pick one, it's The Fifth Race.