Before the Series:
"And Then There Was One" (backup story in Sonic 66)
"My Secret Guardian" (backup story in Super Special 9)
"Eve of Destruction" (backup story in Super Special 9)
"Oh No—Robo!" (backup story in Sonic 0… not really part of continuity, but if it was, it would be here)
Super Special 5: Sonic Kids (except for the backup story "Total Re:Genesis")
Super Special 9: Sonic Kids 2 main story--"ZoneWard Bound"
…
The Early AdventuresSonic 0 main story—"Don’t Cry For Me, Mobius"
Sonic mini-series issue 1
(Mini-series issue 2—"Crowning Achievement" is non-continuity, IMO)
Sonic mini-series issue 2
Sonic 1-17
"Sally’s Crusade" Part 2 (backup story in Sonic 18)
Sonic in Your Face Special
Sonic 18 main story—"Wedding Bell Blues"
Sonic 19-23 (except issue 20’s backup story, "Deadliest of the Species: Prologue")
"Deadliest of the Species" (Sonic 20 backup story, Princess Sally Mini-Series)
Sonic 24
Sonic & Knuckles Special
Sonic 25, 26
Sonic Triple Trouble Special
Sonic 27-29 (29’s backup story, "Growing Pains Part 2" takes place before its’ main story, "Steel Belted Sally")
Sonic 113—"Cry of the Wolf" adaptation
"Growing Pains" (Tails Mini-Series)
Sonic 30
Knuckles Chaotix Special (main story)
Sonic 31-33 (except Knuckles stories)
Super Sonic Vs Hyper Knuckles (main story)
Knuckles backup stories from Chaotix special to SSvsHK special
Sonic 34 - 36
"Rites of Passage" (Knuckles mini-series)
From "The Fall of Robotropolis" to "Endgame"—Freddy’s first saga:
Super Special 8 backup stories ("Running on Empty" & "Ghost Busted")
Sonic 37, 38
Mecha Madness Special
Sonic 40, 41
Sonic Quest Mini-Series
Sonic 42
Sonic Live Special; Sonic 43 (I can never decide which order these two should go in)
Sonic 44
Sonic Blast Special
Sonic 45
"The Map" (Battle Royal backup story)
Sonic 46
"Battle Royal" (Battle Royal main story)
"Endgame" (Sonic 47-49, Sonic Super Special 6: Sonic 50 Director’s Cut)
"Down and Out in Downunda" (Sonic Super Special 4 backup story)
"Brave New World", "Mobius World Tour", and the Knuckles Saga:
Sonic 51, 52
Knuckles Dark Legion Mini-Series
Sonic Super Special 2: Brave New World
"Lost Paradise" (Knuckles 4-6)
Sonic 53
Sonic 54 & 55 / Knuckles 7 & 8 (The stories occur simultaneously)
Knuckles 9
Sonic 56
Super Special 4: Return of the King (main story)
"Total Re:Genesis" (Super Special 5 backup story)
Sonic Super Special 7: Image Crossover
Sonic 57
"The Forgotten Tribe" (Knuckles 10 & 11, Sonic 58, Knuckles 12)
Sonic 56-61 / Knuckles 13-15 (stories occur simultaneously)
Knuckles 16
Knuckles 17 & 18 / Sonic 62-66 (stories roughly simultaneous)
"The Forbidden Zone" (Knuckles 19-21)
"Dark Alliance" (Knuckles 22-24) & Knuckles 25 / Sonic 67 & 68 (stories roughly simultaneous)
Sonic Super Special 8: Zone Wars Prelude (main story)
"Statue of Limitations" (back story in Sonic 70)
Sonic 69 (except Wolfpack story) & 70 / Knuckles 26-28 (roughly simultaneous)
Sonic 71
Sabrina the Teenage Witch 27, 28
Sonic Super Special 10: Crossover Chaos
Sonic Super Special 12: Turnabout Heroes (main story)
"Lupe and the Wolfpack, Part 3" (back story from Sonic 69)
The Rise of Eggman:
"Tales of the Great War" (back stories from issues 71-73)
Sonic 72, 73
"Ascension" (first story of Super Special 11)
Sonic 74-77 (including "Tales of the Great War")
"Tales of the Great War" (back stories in 78 & 79)
Knuckles 29
Sonic Super Special 11: Girls Rule! (except for "Ascension")
"King of the Hill" (Knuckles 30-32)
Sonic 78
"Zone Wars: Giant Robotno" (back story in Super Special 12)
"Law of the Land" (first story in Super Special 14)
"Sonic Adventure" (Sonic 79-82; 82’s main story, "Night of Chaos", is actually the last in this sequence)
Sonic Super Special 13: Sonic Adventure Adaptation
Sonic 83-87
"The Best of Times, the Worst of Times" (second story in Super Special 14)
Sonic 88-93
Sonic Adventure 2 (never properly adapted)
Sonic 99-102
Sonic Super Special 15: Naugus Games
"Myth-Taken Identity" (Back stories in Sonic 103-105)
A Series on Life Support
Sonic 105-123
"Sonic Adventure 2.5" (Sonic 124, 125)
"Tossed in Space" (Sonic 126-129)
"Home" (main stories of Sonic 130-134)
The Tommy Trilogy (Sonic 135-137, starting with 135's "Anoymous")
Sonic 138 - 143
"Love and Loss" (Sonic 144)
"Shadows of Hope", "Training Day" (Sonic 145)
"Out of Your Shell", "Curcuit Me" (Sonic 146)
"Fox and the Hound" (Sonic 147)
"Playing Around" (Sonic 148)
Harbringer (Sonic 145)
GBU (Sonic 146-149)
Destiny's Child (Sonic 148)
The Chosen One - Redux (Sonic 149 - 150)
From Hero to Zero (Sonic 150)
Chaos Emeralds Are Forever (Sonic 151)
Attack of the Nanites (Sonic 152)
Pirate Sally (Sonic 153)
Songoose (Sonic 153 - 154)
More than Meets the Eye (Sonic 154)
Line of Succession (Sonic 155 - 156)
New Blood
Invasion of the Metal Sonics (Sonic 157 - 159)
Birthday Bash (Sonic 160-161)
Sonic Rush (Sonic 160-161)
…
Tales of "the Future":"Mobius 25 Years Later" (Sonic 131-144: 25 years later, though not necessarily in the Mobius Prime Zone)
"Freedom Fighters of the Galaxy" (Sonic 103, 104: 1000 years later, and definitely not in the Mobius Prime Zone)