Friendly Enemy/Web Comics

Wonderella and Hitlerella from The Non-Adventures of Wonderella (who provide the image on the main trope page). So much so that, in the "Death of Wonderella" strip (which parodies both the death of Captain America and the death of Superman), Hitlerella attempts to take up the Wonderella mantle.
- More recently, both had to work to patch up their Friendly Enemy status after going through a rough patch where Hitlerella felt that her enemy didn't care anymore, and Wonderella was bereft to find her fighting other heroes. Hitlerella challenged Wonderella to "Make me wish I'd killed you years ago."
Largo and Ed of Megatokyo
- Ed and Dom too, for that matter.
The majority of the characters on Super Stupor fit this trope, whether they are on the same side or not.
In The Order of the Stick, Minister Malack, who is either Lawful Evil or Lawful Neutral, feels this way about Durkon Thundershield, the cleric on the hero's team. He joins as Durkon's opposite on an evil team because he feels the dwarf "deserves that honor" at the very least, despite deceiving Malack healer. And he gets really upset when Nale orders a poison blast dropped on the area the whole order is in. It would be fair to say that Malack thought of Durkon the way he thought of his own offspring.

Malack: "We agreed Brother Thundershield was not to be harmed!"

Eerie Cuties; Layla and Tiffany are this because Layla has no idea that Tiffany (whom she regards as a BFF) is a Vampire Hunter trying to stake her. Of course, Tiffany isn't very good at it, her attampts on Layla's life so poorly thought out that Layla never even knows Tiffany wants to kill her.