Setting background color/pattern of Inkscape workspace to distinguish transparency
In InkScape 0.48:
File > Document Properties > Page > General > Background
Move R, G, and B to 0. Adjust A (Alpha) to your preference (experiment to set to your liking).
Note that this approach will set the color you choose as the background for the saved/exported image.
In InkScape 0.92:
File > Document Properties > Page > General > Background > Checkerboard background
Since version 0.92 (January 2017) you can instead choose a checkered background. This won't effect the background of the saved image, but will override the background shown in InkScape.
A slight refinement to Carl's answer:
Create a background layer. In it draw a large rectangle of your desired background colour.
Lock the layer to avoid selecting the background rectangle object.
I've written a feature request for this on the Inkscape bug tracker. This is currently not possible, we'll see if it gets implemented in the future.
see https://bugs.launchpad.net/inkscape/+bug/1100755
EDIT Jul 2016: The feature has been added and should be included in the upcoming 0.92 release.