Another vote for Mouseferatu as the Super-Genius (Wil E. Coyote, incumbent). 1E tried to set them up as the magical trickster (Gnome Illusionist/Thief, anyone?), which is partly where the Bard switch in 3.5 came from, but it never was a strong archetype.
I've tried to rehabilitate Gnomes in my homebrew, but my players left them alone.
Gnomes (IMC) are the race of specialists, the race of passion. And I don't mean the romantic Don-Juan passion, but the more general kind. The Passion that breeds fanatics, otaku fanboys, and geeks of every stripe. As the People of Passion, the gnomes can be played for laughs or more seriously, depending on what they obsess over, and how competent they are. They could even be used to play up an alienation theme - because the culture expects/values those gnomes who do find their life's passion, and the earlier the better. In some sense, gnomes are the inverse of the 3e human generalist.
But, as I said, no players ever played a gnome. Darn it.