I know it's an old question, but it's too much fun to pass this one up. There are quite a few examples of wrong ideas that have taken hold, but for the centrality to physics and the degree to which it is wrong and misleading, it is hard to find a better example than the Bohr atom. When it came out, it electrified the physics world on account of its revolutionary viewpoint and stunning success. But eleven years later it became completely obsolete. Nevertheless, in that short time it gripped the imagination of both the physics world and the general public to the point where it remains today the iconic picture of the atom in the minds of just about everyone.

The misleading influences of this model are extremely far reaching. One can begin with the idea of the "quantum leap", which begat wave function collapse, which begat multiple universes et cetera. But perhaps the most persistent holdover of the Bohr atom is the notion that the ordinary laws of electromagnetics must be suspended at the atomic level, otherwise the atom would be unstable. Of course, nothing of the sort is true in modern quantum mechanics, least of all for the hydrogen atom. The greatest triumph of the Schroedinger equation was to show that the motion of electric charge could be tracked through time, and that the stable atomic configurations were precisely those with no accelerating charge distributions. This was an immediate and obvious consequence of Schroedinger's solution for the hydrogen atom.

I would claim that it is not merely true that the stable configurations in QM are those with no accelerating charges. I would go further and suggest that in those cases where the charges do accelerate, the rate at which the kinetic energy of motion is converted into electromagnetic energy is exactly in agreement with that which would be calculated in the ordinary way by applying Maxwell's equations. So, for example, in the case of a black body radiator, if one simply takes the vibrating atoms, accounting for the accelerating motion of the charges, and applies classical antenna theory, you will get the correct black-body spectrum.