This is a great joke. How often do we simply forget that many of the games we play, the side-scrollers at least, are completely two-dimensional? How often do we really stop and think, how is that platform hovering in the air like that? Any why is it I can't go backwards beyond the edge of this imaginary boundary? In fact, one game where all of this is explored is Super Paper Mario, which I personally think is one of the best games for the Wii (as of this writing, of course).
In fact, the conversion between 2-D and 3-D cannot be an easy thing, but I've always been impressed with how well Nintendo did just that with the Metroid Prime series. Not only did they make a successful conversion, but it still somehow maintains the same atmosphere and fun of the earlier Metroid games.
And now I sound like a friggin' advertisement for Nintendo. But, come on, the Wii is awesome, even if the name is a little silly. Rather than trying to make their system faster and more powerful than the competition, they decided to go with something that's generally more fun and easier to use, opening up video games to a much wider audience that doesn't want to figure out what buttom combination allows them to swing a bat.
Anyway, I'm pretty sure I used this two-dimensional comic joke twice more over the course of the comic, once during the Attack of Bob and again during the Return of Bob storyline, though the latter was more of a reference to the former.