Here is a guide that you can use with the archive to jump to specific storylines. The links bring you to the beginning of each storyline.
First Comic and Humble Beginnings: 6/29/01
The Saga of FiredAgain: 7/17/01
Color Gag Strips: 8/8/01
The Superhumans!: 8/29/01
More Gag Strips and the Epic of a Broken Scanner: 9/24/01
Tom Wants to Kill Himself and the Journey to CityTown: 11/26/01
Enter Citytown and the Robot Battle: 1/7/02
The Floating Island of Doom: 6/10/02
Going Home: 9/30/02
Return to the Daily Grind: 11/6/02
The Problem with Stephie: 12/30/02
The Evil Orb: 2/7/03
Wire Needs a Girlfriend and Tom's Return: 7/2/03
Lets Get the Band Back Together and The Breakup: 9/5/03
Astro Zombies: 12/19/03
Tom's Emotional Turmoil and Wire Gets a Bazooka: 3/31/04
Tom Runs Away: 5/19/04
Back to CityTown: 6/18/04
The Trolls of Finland: 7/26/04