How can I make a blank subplot in matplotlib?

A much improved subplot interface has been added to matplotlib since this question was first asked. Here you can create exactly the subplots you need without hiding the extras. In addition, the subplots can span additional rows or columns.

import pylab as plt

ax1 = plt.subplot2grid((3,2),(0, 0))
ax2 = plt.subplot2grid((3,2),(0, 1))
ax3 = plt.subplot2grid((3,2),(1, 0))
ax4 = plt.subplot2grid((3,2),(1, 1))
ax5 = plt.subplot2grid((3,2),(2, 0))

plt.show()

You could always hide the axes which you do not need. For example, the following code turns off the 6th axes completely:

import matplotlib.pyplot as plt

hf, ha = plt.subplots(3,2)
ha[-1, -1].axis('off')

plt.show()

and results in the following figure:

Alternatively, see the accepted answer to the question Hiding axis text in matplotlib plots for a way of keeping the axes but hiding all the axes decorations (e.g. the tick marks and labels).