Broken Base: The 2006 series was rather divisive. On one hand, most of the original actors returned to reprise their roles and it was a straight-up Sequel Series rather than a Continuity Reboot. On the other hand, Limburger and his minions were Demoted to Extra with the Catatonians and Ronaldo Rump replacing them as the main villains.
Ear Worm: The theme song in general is pretty catchy, especially since it's a hard rock theme playing while an echo-y voice chants "Biker Mice from Mars".
Fanon: Vinnie, Stoker, and Carbine are commonly given the respective surnames Van Wham, Van Rotten, and Cannonblade even though none of the Martian mice have official last names.
Genius Bonus: In the 2006 series, Stoker needs Tetra-Hydrocarbons to make a new regenerator. Otherwise known as CH4. Methane.
Ho Yay: Episode 49, where Modo catches Vinnie and the latter makes a comment that makes us all wonder.. And then Modo drops him in the snow.
Jerkass Woobie: Vinnie's old girlfriend Harley becomes this in "Turf Wars", the final episode of the 2006 series. Sure, she wrongly believes that the Biker Mice abandoned her and tries to kill them even when they tell her they need the regenerator to re-hydrate Mars, but it's all because she was horribly scarred during the Plutarkian invasion and nobody showed up to help her. It also helps that she eventually comes to her senses and ends up supposedly sacrificing her life to prevent the regenerator from going critical.
LGBT Fanbase: Muscles, barely any shirts, heroes on motorcycles.. yeah, sounds 'bout right!
Replacement Scrappy: Detractors of the 2006 series tend to see Ronaldo Rump, Dr. Catorkian, Cataclysm, and Hairball as inferior substitutes to Lawrence Limburger, Dr. Karbunkle, Greasepit, and Fred the Mutant respectively.
The Problem with Licensed Games: The PlayStation 2 and Nintendo DS games based on the 2006 series weren't very well-received, mainly because they had difficult controls, a rather generic plot, and, quite confusingly, were released in America about a year before the show it was based on aired in America. Some people, however, are able to look past these flaws and consider them to be decent games in their own right.
They Changed It, Now It Sucks: The opinion of about half the fanbase when they saw the revival series, most of it being because of the new character designs and Lawrence Limburger and his minions being replaced by the Catatonians and Ronaldo Rump as the main villains.