I did this on the old forum and just stumbled across it in my old notes and thought it should be preserved here too:
There are actually several distinct arcs running through DS9:
The Bajoran reconstruction/religion:
101 "Emissary"
(We see DS9 and Bajor in ruins, encounter the Orbs, the Prophets, and find out that Sisko is the Emissary.)
102 "Past Prologue"
(We see that the Federation is not wanted, but needed, as some Bajorans aren't ready to let the war go. Also, we meet Garak, the Cardassian in exile.)
112 "Battle Lines"
(We lose Kai Opaka [and we hear Kira's opinion of her past and Bajor's future].)
114 "Progress"
(Kira is forced to evict an old man from his home in the name of progress.)
118 "Duet"
(A guilt-ridden Cardassian offers himself up to Bajoran justice, causing Kira to question her beliefs.)
119 "In The Hands of the Prophets"
(Vedek Winn does her best to turn DS9 into the Middle East.)
201/202/203 "The Homecoming" "The Circle" "The Siege"
(A Bajoran war-hero returns, and a militant group tries to overthrow the Provisional Government.)
205 "Cardassians"
(A Cardassian child left behind on Bajor is unwillingly repatriated.)
208 "Necessary Evil"
(We get a flashback look at Terok Nor during the Occupation.)
210 "Sanctuary"
(Displaced refugees arrive, and try to settle on Bajor.)
224 "The Collaborator"
(Kira realizes just how much was sacrificed during the Resistance, and Winn becomes the new Kai.)
313 "Life Support"
(Bareil sacrifices himself to establish a treaty between Bajor and Cardassia.)
315 "Destiny"
(Cardassian scientists arrive to establish a relay station, provoking demonstrations, and Sisko & Kira discuss his status as Emissary.)
322 "Explorers"
(Sisko builds an ancient Bajoran star-sailor, confirming an 800 year old connection between Bajor and Cardassia.)
324 "Shakaar"
(Winn tries to tighten her political grip and nearly causes a civil war.)
416 "Accession"
(A time-lost Bajoran claims to be the true Emissary, forcing Sisko to finally embrace the role.)
505 "The Assignment"
(A Pah-Wraith infects Keiko, and Rom[!?] explains Bajoran mythology.)
508 "Things Past"
(Another flashback look at Occupied Terok Nor, and we see that even Odo's hands aren't entirely clean.)
510 "Rapture"
(Bajor nearly joins the Federation, but Sisko sees a vision [presaging the Dominion War].)
511 "The Darkness and The Light"
(A mutilated and crazed Cardassian survivor of the Occupation starts killing off members of Kira's cell.)
601 "A Time to Stand"
(We see DS9 under Dominion Occupation.)
602 "Rocks and Shoals"
(Kira realizes she's become a collaborator.)
603 "Sons and Daughters"
(We see that Ziyal is an artist, who doesn't belong on Cardassia or Bajor, but carries the best elements of both.)
606 "Sacrifice of Angels"
(The new resistance forces the Dominion off DS9.)
611 "Waltz"
(Dukat's facade of sanity falls apart and he escapes, after airing his rationalizations and real opinion of the Bajorans.)
613 "Far Beyond the Stars"
(Sisko receives a vision from the Prophets.)
617 "Wrongs Darker than Death or Night"
(We see another flashback of the Occupation, revealing that the Cardassians kept Bajoran "comfort women.")
621 "The Reckoning"
(Bajoran archeologists trigger an apocalypse. Winn defies the Prophets, admitting that they have never spoken to her [this is probably why].)
626 "Tears of the Prophets"
(Dukat gets possessed by the Pah-Wraith, which then closes the Celestial Temple.)
701/702 "Image in the Sand" "Shadows and Symbols"
(Romulans build an outpost in the Bajoran system and nearly start a war with Kira. Sisko discovers his true parentage and reopens the wormhole. A Pah-Wraith cult has sprung up.)
717 "Penumbra"
(Sisko buys land on Bajor and proposes to Yates. Dukat gets surgically altered to look Bajoran.)
718 "'Til Death Do Us Part"
(Winn receives a vision while Sisko struggles with a Warning. Dukat begins his seduction of Winn.)
719 "Strange Bedfellows"
(Yates gets pulled into Bajoran religious customs. Winn realizes the Pah-Wraiths are pulling her strings.)
720 "The Changing Face of Evil"
(Winn and Dukat conspire to free the Pah-Wraiths.)
721 "When it Rains..."
(Kira, Odo, and Garak join Damar's resistance, but face opposition from Cardassian specism. Dukat is blinded and Winn casts him into the street.)
722 "Tacking Into the Wind"
(Kira runs Damar's resistance with Bajoran know-how.)
724 "The Dogs of War"
(The Dominion shatters the resistance, but Kira still manages to turn it against them because Bajorans Don't Quit. Yates is pregnant.)
725 "What You Leave Behind"
(The Battle of Cardassia. Damar dies, and Cardassia is left in ruins. Dukat and Winn die, and Sisko dwells with the Prophets, but promises to return within a year.)
There are actually several distinct arcs running through DS9:
The Bajoran reconstruction/religion:
101 "Emissary"
(We see DS9 and Bajor in ruins, encounter the Orbs, the Prophets, and find out that Sisko is the Emissary.)
102 "Past Prologue"
(We see that the Federation is not wanted, but needed, as some Bajorans aren't ready to let the war go. Also, we meet Garak, the Cardassian in exile.)
112 "Battle Lines"
(We lose Kai Opaka [and we hear Kira's opinion of her past and Bajor's future].)
114 "Progress"
(Kira is forced to evict an old man from his home in the name of progress.)
118 "Duet"
(A guilt-ridden Cardassian offers himself up to Bajoran justice, causing Kira to question her beliefs.)
119 "In The Hands of the Prophets"
(Vedek Winn does her best to turn DS9 into the Middle East.)
201/202/203 "The Homecoming" "The Circle" "The Siege"
(A Bajoran war-hero returns, and a militant group tries to overthrow the Provisional Government.)
205 "Cardassians"
(A Cardassian child left behind on Bajor is unwillingly repatriated.)
208 "Necessary Evil"
(We get a flashback look at Terok Nor during the Occupation.)
210 "Sanctuary"
(Displaced refugees arrive, and try to settle on Bajor.)
224 "The Collaborator"
(Kira realizes just how much was sacrificed during the Resistance, and Winn becomes the new Kai.)
313 "Life Support"
(Bareil sacrifices himself to establish a treaty between Bajor and Cardassia.)
315 "Destiny"
(Cardassian scientists arrive to establish a relay station, provoking demonstrations, and Sisko & Kira discuss his status as Emissary.)
322 "Explorers"
(Sisko builds an ancient Bajoran star-sailor, confirming an 800 year old connection between Bajor and Cardassia.)
324 "Shakaar"
(Winn tries to tighten her political grip and nearly causes a civil war.)
416 "Accession"
(A time-lost Bajoran claims to be the true Emissary, forcing Sisko to finally embrace the role.)
505 "The Assignment"
(A Pah-Wraith infects Keiko, and Rom[!?] explains Bajoran mythology.)
508 "Things Past"
(Another flashback look at Occupied Terok Nor, and we see that even Odo's hands aren't entirely clean.)
510 "Rapture"
(Bajor nearly joins the Federation, but Sisko sees a vision [presaging the Dominion War].)
511 "The Darkness and The Light"
(A mutilated and crazed Cardassian survivor of the Occupation starts killing off members of Kira's cell.)
601 "A Time to Stand"
(We see DS9 under Dominion Occupation.)
602 "Rocks and Shoals"
(Kira realizes she's become a collaborator.)
603 "Sons and Daughters"
(We see that Ziyal is an artist, who doesn't belong on Cardassia or Bajor, but carries the best elements of both.)
606 "Sacrifice of Angels"
(The new resistance forces the Dominion off DS9.)
611 "Waltz"
(Dukat's facade of sanity falls apart and he escapes, after airing his rationalizations and real opinion of the Bajorans.)
613 "Far Beyond the Stars"
(Sisko receives a vision from the Prophets.)
617 "Wrongs Darker than Death or Night"
(We see another flashback of the Occupation, revealing that the Cardassians kept Bajoran "comfort women.")
621 "The Reckoning"
(Bajoran archeologists trigger an apocalypse. Winn defies the Prophets, admitting that they have never spoken to her [this is probably why].)
626 "Tears of the Prophets"
(Dukat gets possessed by the Pah-Wraith, which then closes the Celestial Temple.)
701/702 "Image in the Sand" "Shadows and Symbols"
(Romulans build an outpost in the Bajoran system and nearly start a war with Kira. Sisko discovers his true parentage and reopens the wormhole. A Pah-Wraith cult has sprung up.)
717 "Penumbra"
(Sisko buys land on Bajor and proposes to Yates. Dukat gets surgically altered to look Bajoran.)
718 "'Til Death Do Us Part"
(Winn receives a vision while Sisko struggles with a Warning. Dukat begins his seduction of Winn.)
719 "Strange Bedfellows"
(Yates gets pulled into Bajoran religious customs. Winn realizes the Pah-Wraiths are pulling her strings.)
720 "The Changing Face of Evil"
(Winn and Dukat conspire to free the Pah-Wraiths.)
721 "When it Rains..."
(Kira, Odo, and Garak join Damar's resistance, but face opposition from Cardassian specism. Dukat is blinded and Winn casts him into the street.)
722 "Tacking Into the Wind"
(Kira runs Damar's resistance with Bajoran know-how.)
724 "The Dogs of War"
(The Dominion shatters the resistance, but Kira still manages to turn it against them because Bajorans Don't Quit. Yates is pregnant.)
725 "What You Leave Behind"
(The Battle of Cardassia. Damar dies, and Cardassia is left in ruins. Dukat and Winn die, and Sisko dwells with the Prophets, but promises to return within a year.)