Why does the direction of a dipole moment go from negative to positive charge?
There are two separate issues here. (1) Why does it make sense to consider a dipole moment as a vector? (2) Given that it's a vector, why does it make sense to say that it points in this particular direction, rather than the opposite direction.
Intuitively, it makes sense to define a dipole as a vector because when we put it in a field, it aligns itself with the field like a little arrow. Fundamentally, we treat things as vectors when they transform as vectors. We have monopoles, dipoles, quadrupoles, ... Monopoles (electric charges) don't change under rotation, so they're scalars. Dipoles reverse themselves under 180 degree rotation, so they're vectors. Quadrupoles reverse themselves under 90 degree rotation, so they're tensors.
This is purely a matter of convention. According to the usual convention, the potential energy of an electric dipole is $-\mathbf{p}\cdot \mathbf{E}$. Historically, whoever first defined the dipole moment could have defined it with the opposite sign. Then the energy would have been $+\mathbf{p}\cdot \mathbf{E}$. The sign would also have been reversed in every other equation, e.g., $\boldsymbol{\tau}=\mathbf{p}\times \mathbf{E}$ would have become $\boldsymbol{\tau}=\mathbf{E}\times \mathbf{p}$.
There are many, many arbitrary choices of sign like this in physics. If Ben Franklin had made the opposite choice for the sign of the charge of cat fur rubbed on glass (or whatever it was he used as a standard), then we'd say today that electrons had positive charge. The direction of the magnetic field is also arbitrary and could have been defined as pointing the opposite way (in which case some of the signs in Maxwell's equations would flip).
I don't agree with Ben Crowell. I think that the reason that the moment is directed from negative to positive is because of the definition of moment:
$$ \mathbf{p} = \sum\nolimits q*\mathbf{d} $$ q: charge, d:distance from the origin of coordinates to the carge
If you have a negative and positive charge, this relation gives you the direction from negative to positive.