Summary:

Assume that

import matplotlib.pyplot as plt

has been executed.

When using mplot3d in IPython you have to manually draw the axes which can be done using the plt.draw function (or plt.plot([],[])).
For some reason the axes are not automatically drawn as with 2d plots.

The full story:

IPython provides some nice functionality for interactive plotting. For instance, the code

import numpy as np
import matplotlib.pyplot as plt

x = np.linspace(0, 2*np.pi, 100)
y = np.sin(x)
plt.plot(x, y)

pops up a figure with the graph of the sin function over the interval $[0,2\pi]$.

When using mplot3d for 3d plots in IPython the constructed axes are not drawn by default. For instance the code (taken from the mplot3d examples)

import numpy as np
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt

def randrange(n, vmin, vmax):
    return (vmax-vmin)*np.random.rand(n) + vmin

fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
n = 100
for c, m, zl, zh in [('r', 'o', -50, -25), ('b', '^', -30, -5)]:
    xs = randrange(n, 23, 32)
    ys = randrange(n, 0, 100)
    zs = randrange(n, zl, zh)
    ax.scatter(xs, ys, zs, c=c, marker=m)

ax.set_xlabel('X Label')
ax.set_ylabel('Y Label')
ax.set_zlabel('Z Label')

plt.show()

results in a blank figure on the screen. In order to see the results one must manually draw the axes which can be done with the plt.draw function (or with plt.plot([],[])). I have no idea why this is the case, but hopefully it will be fixed at some point.