The model of time travel used in StickManStickMan was chosen to be as logically consistent as possible.

Travelling forwards in time for a hundred years is effectively the same as simply vanishing without trace for a hundred years and then reappearing. This presents no causal problems as far as paradoxes etc. are concerned. Travelling backwards in time has a completely different effect. Whenever you go backwards in time, your re-emergence into the real world "nudges" the universe onto a different timeline. This is because you have changed something: just by appearing in the past, that has changed the universe and you are now in a different universe from the one you began in. You are now free to kill your own grandfather etc. without fear of paradox, because this is a different timeline entirely. Basically, a man who goes backwards in time never returns to the universe he started from.

The StickManStickMan chronicles begin in Timeline A and follow the adventures of the guys who were born in that timeline, known as the "A-guys". (There are of course infinitely many other guys, whom we don't follow.) In accordance with the theory, whenever the guys travel backwards in time, the universe diverges in two. So far in the chronicles they have travelled backwards in time three times, creating Timelines B, C and D. Currently they are in Timeline D, and if they ever travel back in time again they will presumably end up in Timeline E.

NOTE: comics occur roughly on the date they were first uploaded, but not exactly. Obviously, it's not as if 24 hours pass between each comic, or each conversation would go on for weeks.

It's a confusing diagram but it's fairly easy to follow the guys' journey. First, trace down Timeline A, ignoring divergences, until you reach the point in 2002-A when they first jump backwards in time. Now go backwards in time and shift over into Timeline B, then carry on tracing down, this time all the way to 3001-B. Go back again, and shift over to Timeline C. Follow down to 2033-C and jump back again, into Timeline D.

There are a few references to what happens differently in the timelines that the guys leave behind, included to clear up some temporal plot holes which I discovered while I was putting the timeline together.

BC 2,508,412,235,991 Creation of Universe -1.
BC 1,000,237,299,576 A collection of powerful civilizations gather together for Project Unlimit; an attempt to genetically engineer a Super-Tetris 3 gamer.
BC 1,000,237,299,125 Project Unlimit has its first success: the being later known as the Oracle is born and attains STL3 soon afterwards.
BC 1,000,237,299,119 Zero is born. He is much stronger than the Oracle; a creature of pure malevolence who wreaks havoc on his home galaxy.
BC 1,000,237,299,094 Zero is captured. A small portion of Universe -1 is separated off and becomes Universe 0, with Zero trapped inside it.
In the next aeons Several more STL3 gamers are created, none of them as malevolent as Zero. Because of their immortality they outlive their own civilizations and the universe itself.
BC 16,237,845,156 The Oracle is among the STL3 gamers of Universe -1 as they gather together to witness the Big Crunch.
In the instant between the Big Crunch and the Big Bang, they restructure the universe's physical laws so that it is no longer possible to reach STL3.
Universe 1 begins with the Big Bang.
The STL3s disperse themselves among the new universe.
???? The stargate network is first constructed by an unknown race.
"Aeons" ago The Doctor encounters Riaa.

DIVERGENCE: Timeline B splits off from Timeline A.

BC 149,977,208 Jurassic Earth has a near miss with an asteroid. The A-guys and the Doctor arrive from 2002-A just in time to witness the near miss. Next stop, BC 2479-B.
BC 3119 The STL3 gamers of the universe discover that Universe 0 still exists and is curving around on a collision course with Universe 1.
The Oracle is dispatched to the Milky Way galaxy (Zero's arrival point) to prepare to defeat him once and for all.
BC 2490 The fourth dynasty pharaoh Menkaure, son of Khafre who had the Sphinx constructed, comes to power in Egypt.
BC 2479 In ancient Egypt, the nose falls off the Sphinx. The A-guys and the Doctor arrive from BC 149,977,208-B just in time to get the blame for it. Next stop, AD 3001-B.
BC 2472 Menkaure dies.
BC 110 The Oracle selects Mankind as the race most likely to produce a gamer capable of beating Zero. He heads for Earth.
BC 105 The Oracle foresees the birth of Freecell, whom he predicts will be the greatest gamer in the galaxy at the time of Zero's return. He writes the Book, intending for it to guide Freecell on the path to becoming as powerful as possible.
AD 1681 The Eight Death Crystals are first created. They will unleash hordes of evil every 1,000 years.
November 2, 1911 Douglas McGuire invents the Moon.
November 6, 1952 Birth of Shigeru Miyamoto.
1972 A crack commando unit is sent to prison for a crime they didn't commit.
June 11, 1973 Birth of Guy Stanley Mienczakowski A. Freecell is born on the same day. Birth of Guy Stanley Mienczakowski B.
1975 Birth of Guy Michael Littler A. Birth of Guy Michael Littler B.
September 15, 1992 In real life, the date of the very first StickManStickMan comic.
May 1993 Asul Dlang is born.
August 1998 Guy Mienczakowski meets Tina Miller at a Mario Kart tournament.
August 1999 Guy marries Tina.
early September 1999 Tina Mienczakowski is imprisoned for four years for smuggling Tic-Tacs into Burundi.
March 2001 Guy Mienczakowski moves in with Guy Littler.
July 2001 The guys have a headcrab problem in their basement and have to get an exterminator in.
September 2001 Super Monkey Ball, containing subliminal messages provoking banana cravings, is launched in Japan.
December 2001 The guys independently invent cheese on toast.
January 2002 UN orders worldwide purge of stickman comics.
February 1, 2002 Guy Littler acquires his self-destruction power.
In real life, StickManStickMan is launched.
February 3, 2002 Guy Mienczakowski goes Super-Tetris for the first time.
February 11, 2002 Quake 3 deathmatch. Guy Mienczakowski goes Super-Tetris Level 2 and beats Freecell by fluke.
Guy Littler first becomes Antman.
The guys have their pizza-related adventures and their first encounter with Asul, aged 8.
(Yes, a lot can happen in a day.)
early March 2002 Angered by his defeat at the hands of Guy Mienczakowski, Freecell begins training to become Super-Tetris Level 2 and amassing an army of the l33t.
Chocolate Coated Bullets become one-hit wonders with "Chips For Tea".
mid-March 2002 Chocolate Coated Bullets are blasted into space. They spend 8 days on the Moon, and one of them drops a frisbee on Riaa's territory around Mount Pico. Riaa begins following the guys.
late March 2002 The guys go to Area 51, end up in a conflict with the Quingi and crashland in Las Vegas.
The Quingi return to destroy Earth but are defeated.
May 3, 2002 Super Monkey Ball is launched in the UK. Guy Mienczakowski buys a copy and slowly starts to become addicted to bananas.
June 2002 The A-guys and the Doctor engage in a little time travelling. They head to BC 149,977,208-B, never to return to Timeline A. The B-guys and the Doctor engage in a little time travelling. They head to BC 149,977,208 in another timeline, never to return to Timeline B.

DIVERGENCE: Timeline C splits off from Timeline B.

June 2002 Ray never meets the guys, and whiles away his years bungee jumping instead.
The Quingi Emperor finds that the guys are no longer on Earth, and leaves, dissatisfied.
The A-guys return from 3001-B after their adventures with the Doctor.
Later that day they enjoy some bungee jumping and meet Ray, the super-intelligent alligator. They help Ray win on Who Wants To Be A Millionaire?. Ray goes on to pursue a career in politics.
Meanwhile the Quingi Emperor constructs a base in the middle of the Atlantic.
July 2002   Guy Littler buys a new computer and is briefly smitten with dreams of megalomania, until James Bond arrives to stop him. The guys help out with the filming of his new movie, both starring as James Bond.
Meanwhile, the Quingi Emperor begins to put together the Band Of Supervillains.
August 2002 Addictive chemicals are detected inside bananas, which are then made contraband by the UN.
September 2002 Martin the monkey flees the army after being caught nibbling contraband bananas.
November 8, 2002 The new Bond flick, Jawbreaker, is set back because of the lack of a leading man. The guys attend the star-studded premier of the new James Bond movie, "Jawbreaker".
Two messages are left on the guys' answerphone. The first is from Gordon Freeman. The second is from King Arthur, who has been hired by the Quingi Emperor to destroy the guys.
The guys answer the first message immediately and head off to help Gordon save the world. The second message is left unanswered for six months.
December 3, 2002   Vaultland secedes from the main United Kingdom and becomes its own country. Vaultlandic Independence Day.
late December 2002   The guys compete as the Vaultlandic team in Honolulu Winter Olympics.
early January 2003   The A-guys fly home after the Honolulu Winter Olympics. Their flight encounters a temporal storm and is instead hurled thirty years forward in time, to 2033-C.

DIVERGENCE: Timeline D splits off from Timeline C.

early February 2003 Freecell has by this time risen to become the greatest gamer in the world (indeed, the galaxy). Without opposition, he rises up and begins to conquer and unify the globe with his army of the l33t. The guys never come home. Freecell destroys Vaultland utterly, and, without opposition, begins to conquer the globe with his army of the l33t. The A-guys return through time after their journey to dystopic 2033-C. Freecell attacks Vaultland just as they arrive home, but they defeat him again.
March 2003   Short of bananas, the guys meet Martin and subsequently uncover and put a stop to Nagoshi's banana conspiracy.
With Freecell dead, The Oracle attempts to salvage what he can of his plan to defeat Zero. He selects Guy Mienczakowski as the new One.
April 2003   After a brief timeloop, Guy Mienczakowski buys a monolith which attempts but fails to take over the world.
late April 2003   The guys stumble upon the Sixth Death Crystal, but cast it aside. Riaa snatches it up and begins acquiring the remaining seven.
early August 2003   The guys listen to their second answerphone message, and set off to meet King Arthur.
mid-August 2003   The guys meet and capture Andre.
late August 2003   The guys return to Arthur and defeat him, meeting Asul again on the way, now 10 years old.
Cheesequake/Colonel Thirty-Two attacks them on the way home but they defeat him too.
early September 2003   Asul and the guys go to the CIA for help in defeating the Band Of Supervillains. Still wanted for noise pollution, they are chased and briefly locked up, where they meet Tina. All are soon released, including Tina, who has now served her four years.
mid-September 2003   The CIA and the American Navy help the guys with an undersea expedition to destroy the Quingi Emperor.
The Quingi Emperor promises his race's return one year from now, in September 2004.
The guys meet some giant squid.
late September 2003   Riaa frames the guys for destroying the internet.
Google Labs begin searching for a backup copy of it.
January 2004   King Squid of the Calimar becomes President of the United States of America.
March 28, 2004   The guys meet Riaa.
Guy Littler destroys the Moon.
The guys pursue Riaa through a stargate to 2681-D.
Tina, Asul and Google Labs restore the internet from a backup copy.
September 2004   The new Quingi Emperor arrives to take his revenge on the guys. Tina persuades him to leave.
Tina cryogenically freezes herself so that she can see her husband again.
October 26, 2004 In real life, StickManStickMan finishes.
2033 Freecell's iron l33tocracy has now long dominated the globe.  
January 2033   The guys emerge from 2003-C into the dystopic Freecell future. They destroy Freecell.
With the help of 81-year-old Shigeru Miyamoto, and as prophecied in The Book, The One restores the balance of gaming.
The guys return home to 2003-D a few weeks later, never to return to this dystopic universe.
2034 Freecell learns he is The One and leaves Earth for Omrexis-1. Earth's political structure begins to revert to normal. Earth's political structure begins to revert to normal.  
???? Cold War 2 begins between global superpowers Iceland and Madagascar.
Huge sentient flies are created as a byproduct of the military buildup.
???? World War 3 occurs between Iceland and Madagascar.
Giant squid step in and take over world leadership.
2652 Mars begins campaigning for independence from its Terran founders.
2681 The Eight Death Crystals are first scheduled to unleash their hordes of evil.
July 10, 2681 After 29 years of increasing hostilities, World War IV between Earth and Mars begins. Earth is destroyed by a Martian doomsday weapon. The guys arrive here from 2004-D. They save Earth from being destroyed and use the Quingi fleet to enforce peace on both planets.
July 12, 2681   Tina and the guys arrive on Omrexis-1.
July 13, 2681   Guy Mienczakowski begins receiving implants and enhancements to make him fight better.
July 15, 2681   The Oracle visits Guy Mienczakowski and gives him the power to reach Super-Tetris Level Three.
July 17, 2681 On planet Omrexis-1, Universe 0 reconnects with Universe 1 and Zero is set loose.
Freecell attains Super-Tetris Level Three and defeats Zero. Zero is unleashed on the galaxy. Guy Mienczakowski and Guy Littler defeat Zero.
3001   Travelling forwards in time from BC 2479-B, the A-guys and the Doctor appear briefly at a Martian spaceport. They then return to June 2002-C, never to visit Timeline B again.