A coloring error caused Precocious' Yvette to suddenly appear darker for a few days (compare her in this strip to her the next day). The author decided that she looked better this way and kept the new "dark Yvette"
A one-panel example in Concerned: author Chris Livingston was in the middle of making a strip when his wife made the off-the-cuff request that, at some point of the comic's run, protagonist Gordon Frohman use the expression, "Eep". Livingston promptly put the expression directly into the panel he was working on at that exact moment — thus having Gordon say "Eep" in response to getting blasted in the chest with a shotgun.
Domain Tnemrot: The referee was never meant to be named and would just be a background character. Fans loved him, so he was given a bigger role.
Many elements of Digger, including major characters and plot points, were invented on the spur of the moment.
When the Commander and Jonesy went to the future in Manly Guys Doing Manly Things, the chaos left behind in the present was originally just going to be generic chaos, but then Twitch Plays Pokémon Red came out and Coelasquid was inspired to make a homage to it instead.