How do I visualize an atom?
I have searched and searched, oh how I have searched.


Do you know what I always tell my mom when she asks me to find something in the Internet she was not able to find herself? I ask her: "Are you sure that the thing you are looking for even exists?"


  I am looking for a 3 dimensional visualization of a whole (moderately
  complex, hydrogen is just a ball) atom that includes 3 dimensional
  orbital geometry.



Hydrogen atom is not "just a ball".
There is no orbitals. In short, except for one-electron systems (such as the hydrogen atom) orbital description is just an approximate model of the reality.
Usually when one asks to visualize a physical object, he/she wants to visualize its physical "boundaries" with respect to some medium. The notion of such "boundary" simply looses its meaning in the microscopic world: atoms do not have "boundaries" like macroscopic objects do.



  Please. The universe is weird and I want to see.


Sorry, but you can not do this: you can not visualize some things in the Universe, you can not even imagine them. Our visualization &amp; imagination abilities (unlike an atom) has some boundaries, because they are based ultimately on our senses which in turn has their boundaries.

As Paul Dirac said on that matter:


  […] the main object of physical science is not the provision of
  pictures, but is the formulation of laws governing phenomena and the
  application of these laws to the discovery of new phenomena. If a
  picture exists, so much the better; but whether a picture exists or
  not is a matter of only secondary importance. In the case of atomic
  phenomena no picture can be expected to exist in the usual sense of
  the word 'picture', by which is meant a model functioning essentially
  on classical lines. One may, however, extend the meaning of the word
  'picture' to include any way of looking at the fundamental laws which
  makes their self-consistency obvious. With this extension, one may
  gradually acquire a picture of atomic phenomena by becoming familiar
  with the laws of the quantum theory.