Setup: Anaconda 2.0.0 (Win 64), Spyder (2.3.0rc that came with Anaconda)
I configure the graphics: Tools > Preferences > iPython console > Graphics > Graphics backend > Inline
But no matter what I do the graphics always open in a separate window? Is there a way to force them to be inline in the console?
From Spyder 4.0, figures now render in the new Plots pane by default, so the answer in the comments is outdated - for the benefit of people viewing this question in the future; figures can now be plotted inline by unchecking the "Mute Inline Plotting" option from the menu in the top-right of the Plots pane, as shown below.