Season four of Stargate continues the trend of marginalizing the single episodes, who either serve to further the continuity-laden episodes or present rather boring takes on the evil local government. Either you get the obviously bad guys from the start or things turn out to be less than positive (a disease which plague the various Star Trek series as well). But as with the previous season, at least two of the single episodes were quite good (Window of Opportunity and Entity).
Window of Opportunity is pretty much Groundhog Day with Jack O’Neill and Teal’c. Entity is a typical first-contact-gone-wrong story with interesting aliens (although the radio wave induced destruction sounded pretty stupid, a more convincing explanation would have been that the data itself was the cause for the aggression of the aliens, which incidentally reminded me of how the aliens in Peter Watts Blindsight reacted to human communication attempts).
Season four also acts like a break for the eight-season Goa’uld arc, as the big bad of the first four seasons gets his comeuppance. With the destruction and assimilation of Sokar’s dominion, Apophis has reached a level of power unprecedented before. And then, something comes along to whom Apophis power base is still nothing more than a tasty snack (the replicators of course). The power-asymmetry between Apophis and the replicators is on a similar order as between the Goa’uld and the human cultures they subjugated. IMHO, the perfect end for Apophis (thankfully it really was the end and they didn’t go for reviving him a second time).
Actually Apophis gets killed in the second episode of the fifth season, but due to the nature of the cliffhangers at the end of each season on Stargate, I include episodes that conclude these cliffhangers as part of the previous season.