I got this from someone at SonicRetro because it made the most sense in terms of explaining the Sonic the Hedgehog Timeline though I've made some slight changes to it.
"Universe 0" Sonic 1 Proto?
"Original universe" GameGear / Master System Sonic Games --> 06 -->
"Soft reset of the universe 1" * --> SegaSonic --> 1 --> CD bad future --> 2 --> 3nK --> Adventure 1 --> Advance 1 --> Adventure 2 --> Advance 2 --> Heroes --> Battle --> Advance 3 --> Shadow --> [Elise feels the wind in 06's ending] --> Secret Rings --> Rush --> Black Knight --> Unleashed --> Rush Adventure --> Colours --> Generations -->
"Soft reset of the universe 2" ** --> SegaSonic --> 1 --> CD bad future --> 2 --> 3nK --> Generations --> 4e1/Tails Adventure --> 4e2 --> [possibly 4e3 OR the Fighters, but not both] --> Adventure 1 --> Rush --> Unleashed --> Rush Adventure --> Colours --> Generations --> [Continued feedback into the 2nd soft reset] --> Lost World --> [???] Sonic Runners?
"Alternate universe 1" Sonic Eraser (Takes place in Sonic's mind or possibly a simulation / experiment designed by Tails or Eggman?)
"Alternate universe 2" Dr. Robotniks Mean Bean Machine --> Adventures of Sonic the Hedgehog TV Show
"Alternate universe 3" Sonic Spinball --> ???
"Alternate universe 4" Sonic 3D Blast / Flickies Island --> ???
"Alternate universe 5" Sonic Drift 1 --> Drift 2 --> Sonic R --> Riders --> Riders 2 --> Free Riders --> ??? (Sega Allstars Racing?)
"Alternate universe 6" Sonic Chronicles the Dark Brotherhood (Eggman wins unless a sequel is made)
"Alternate universe 7" Sonic Rivals 1 --> Sonic Rivals 2 (not sure if these 2 are cannon or not)
"Alternate universe 8" Sonic Boom Rise of Lyric --> Sonic Boom TV Show? (Eggman grabs something in the end of the game and is seen wearing it in the show)
"Alternate universe 9" Sonic Boom Shattered Crystal --> Sonic Boom Comics? (I'm guessing on this one)
*Eggman's interactions with Sonic and co in the original universe- existing as inklings of memories- give him a serious upper hand. It alerts him to the existance of the Echidna tribe (bringing Angel Island and Chaos to his awareness), greater knowledge of time travel (which allows him to track down and chain the Little Planet for easier control of the flow of time), knowledge that GUN have Shadow in their possession and being able to intervene earlier to stop the black hedgehog being used against him, and knowledge that Sonic is his nemesis in advance, leading him to track down and attempt to destroy his future nemesis before he'll be a pain in the butt in the first place. Also, the freeing of the seventh Chaos Emerald from its unstable time loop (thanks BlackHole!), allowing the stakes to be raised significantly.
**Classic Sonic is re-inserted into the timeline at the end of S3nK, his earlier-than-usual Homing Attack development seriously derailing the timeline. Specifically, he's rocked enough by this newfound knowledge of his future self that he goes off on his own, splitting from Tails for a bit- and discovering Eggman's trying to take control of the Little Planet once again. In the original soft reset universe, Eggman conquered the Little Planet without Sonic knowing, scorching its surface so it would be the barren moon seen in the beginning of Sonic Adventure 2... having been his grandfather's ARK this entire time. Sonic's defeat of Eggman and reclaiming the Little Planet a second time would mean Shadow is never revealed from his slumber in this timeline, would remove the events of Adventure 2 to Shadow entirely, and would mean Shadow only shows up in Generations onwards thanks to the soft reset universe timeline. This would explain his absence from the original party at the beginning of Generations. His presence in 06 from the original universe could be explained as GUN using Shadow (who they had in storage at the beginning of SA2) as a weapon against Eggman.
I know that there's some games missing so if you know which ones let me know.
I excluded crossovers because those takes place in their own separate universe same for the comics too.
The tv shows Adventures of Sonic the Hedgehog, Sonic SatAM, Sonic OVA, Sonic Underground and Sonic X takes place in their own separate universes.
Do you agree?
What would your headcannons be?