1. John’s ten minutes sooner in his rescue mission; Sumner doesn’t die, doesn’t meet the Wraith queen, doesn’t share John’s rapport with the Athosians.
(Alternately, they find old!Elizabeth sooner, and are able to get their hands on a couple of still-charged ZPMs; the season finale goes a bit differently.)
2. Slightly more honest and charitable handling of Michael turns him into an ally, and gains the expedition a thorough understanding of how Wraith society and technology work.
3. They find the Aurora before the Wraith saboteur gets on board, and are able to win the captain’s trust and access to the report of the Wraiths’ weakness; Rodney gets to work (virtually) with real live Alteran engineers.
4. The Atlantis crew arrives before the Travellers (and John is a bit more wary around Larrin), allowing them to claim and keep the Alteran ship.
(Alternately, Rodney and the SGC are less stupid about security, and the whole Midway fiasco doesn’t happen.)
5. They find and refurbish a derelict ancient gate-seeding ship (complete with gates!), planning on using it for ferrying duties so that Earth’s ships can focus on protecting Earth. But on the maiden voyage something goes wrong (and the writers do a lot of hand-waving), stranding ship and crew waaaaaay back in the past. Right around the time when the gate system would have been going up....
(Why yes, I’ve watched only a couple episodes of season five. Don’t look at me like that.)