- s01ep10 The Torment of Tantalus - Daniel Jackson discovers that the Stargate was activated in 1945 and a young professor went through, never to return. Together with his still living fiancée, the SG1 team discover the now aged professor, naked and trapped in a decaying fortress, containing the secrets of an Ancient alliance. Will they be able to rescue him and escape to earth in time?
- s02ep15 The Fifth Race - SG-1 travels to a planet whose people are allies of the Asgard.
- s03ep18 Shades of Grey - Col. O'Neill is dismissed from the SGC for stealing alien technology and is subsequently approached to participate in an even more covert Stargate operation.
- s04ep6 Window of Opportunity - Col. O'Neill and Teal'c realize they and their friends are trapped in a time loop.
- s05ep02 Threshold - SG-1 asks Bra'tac to help clear Teal'c's brainwashed mind. Bra'tac removes Teal'c's symbiote and Teal'c is forced to remember certain memories of his past in order to get back to the real Teal'c in the end. SG-1 is glad to have him back.
- s06ep06 Abyss - O'Neill's symbiont Kanan drags him to a planet ruled by the Goa'uld Ba'al, where Kanan was undercover. Ba'al captures and tortures O'Neil, whose only hope may lie with - Daniel Jackson?!?
- s07ep17 & ep18 Heroes - The president has asked that a documentarian go to SGC to create a film about its operations. His arrival is unwelcome to most and he begins to clash with the base personnel. Nevertheless, he conducts his interviews with SG-1 and the scientists in the employ of SGC. Meanwhile, an off-world SG team finds the remains of an Ancient city.
- s08ep16 & ep17 Reckoning - After a long absence, Jacob Carter returns to the SGC to tell Jack that the galaxy is under threat of takeover by the Replicators.
- s09ep06 Beachhead - A Prior of the Ori has established an ever-growing forcefield on a Jaffa-controlled planet called Kalana. A minor Goa'uld named Nerus, who engineered the multiple Gate connections required for the defeat of the Replicators, comes to the SGC with information on the event and offers his help.
- s10e10 & e11 The Quest - During their quest for the Sangraal, SG-1 must join forces with their enemy and face a real-life dragon.
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The episodes included above are not necessarily the best ones, just the ones I enjoyed the most and expand the overall story arc. The following is a list of runners-up that rank highly or are interchangeable with the episodes above. These aim to complete ongoing Earth-based story arcs vs the galaxy level events so are ranked highly on their own as well. I know technically Heroes is the exception but it does contrast well with episodes like the loss of Daniel up to the point that Dr Frasier doesn't actually return as a permanent cast member after her loss...
- s01ep01&02 Children of the Gods - Colonel Jack O'Neill is brought out of retirement to lead a new expedition back to Abydos, only to find an old friend, a new enemy and a far wider use of the Stargate.
- s04ep16 Chain Reaction - General Hammond mysteriously retires from the SGC and a new general is brought in, who breaks up SG-1.
- s05ep21 Meridian - As Jackson suffers from a fatal dose of radiation, he struggles with the value of his life while his friends deal with the emotional and diplomatic repercussions.
- s06ep14 Smoke & Mirrors - Senator Kinsey is shot in the chest at a public event, killing him just before his party's presidential nomination. Jack is arrested for the murder, and General Hammond assigns the rest of SG-1 to uncover the truth.
- s06ep17 Disclosure - The US and Russia reveal Stargate Command and its operations to representatives of the other permanent members of the United Nations Security Council.
- s07ep20 Inauguration
- s09ep10 & ep11 The Fourth Horseman - The Ori unleash a deadly plague on Earth, prompting a powerful ally from SG-1's past to come to their aid.
As far as just plain fun episodes go, any where O'Neill interacts with Maybourne and/or Kinsey is awesome along with the episodes for Mitchel with Jup and Tenat.