I've recently switched from Enthought Canopy to Anaconda and am using the Spyder IDE. I've noticed that when I plot some data,
import matplotlib.pyplot as plt
Select from the menu
Tools > Preferences, then
IPython console in the list of categories on the left, then the tab
Graphics at the top, and change the
Graphics backend from Inline to e.g. Qt.
For me though, the figures then always pop up in the background.
(I use Spyder 3.0.0dev bundled with WinPython 3.4.)