Software update hangs on OS X Snow Leopard - how can I fix it?
Fixed

I was able to fix this problem by downloading and running the Mac OS X 10.6.8 Update Combo v1.1.

After this ran and I restarted, I was able to successfully run Software Update, from the command line or the GUI; it now tells me that there is no new software to install.

Before doing this, I did check for I/O errors as @SethNoble suggested, then run the utilities that @Stephen suggested. I did not find any problems, although I had previously run Disk Utility from my OS X install disk and repaired both permissions and files.