To add a spacer to the applications (left) side of the Dock, run the following in the terminal:
defaults write com.apple.dock persistent-apps -array-add '{tile-data={}; tile-type="spacer-tile";}'
To see your changes, restart the dock with killall Dock.
To add a spacer to the documents (right) side of the Dock, run the following:
defaults write com.apple.dock persistent-others -array-add '{tile-data={}; tile-type="spacer-tile";}'
Again, killall Dock to see your changes. Once the spacer is in the Dock, you can drag it around to move it. You can even drag it between the application and document sections, if you wish. Run either command multiple times to add multiple separators.
[robg adds: I tried this in 10.4, but it's definitely a 10.5-only hint, and it works as described -- the image above is from my machine. It seems this ancient hint can finally be retired (though the spacers are a bit wider than I would prefer, if I actually used the Dock much).]
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