I was playing around in Unity 2D, and I messed up my configuration. How can I reset it, preferably without losing other config files? (such as Empathy config, Firefox/Chrome config, etc)
3 Answers
Open a terminal and type
dconf reset -f /
to reset Unity 2D to defaults, or IMPORTANT - THIS RESETS EVERYTHING NOT JUST UNITY-2D
unity --reset
to reset Unity (3D).
If default Ubuntu Nautilus theme is also missing, close all instances and type
rm -R ~/.gconf/apps/nautilus

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Although this link may seem off topic, it covers some of the information I believe you are looking for.
Edit: Whoops, I see fossfreedom was already on the case.
Changing Unity Default Settings
User: fossfreedom points out,
The list of sessions is described in the directory:
/usr/share/xsessions
For unity-2d the session file is called:
ubuntu-2d.desktop
fossfreedom goes on to explain how to reset this to default. Hopefully, this method would leave your files intact.
Regards, SomaComa
To reset unity type the following in the terminal:
unity --reset
To reset the unity icons type:
unity --reset-icons
To reset Compiz type (NOTE: this will reset ALL compiz settings):
gconftool-2 --recursive-unset /apps/compiz-1
unity --reset
The above command will reset the respective elements back to their default configuration.

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1Nope, that's for normal Unity. This is for Unity 2D, not 3D. Thanks for the answer though, it's already documented here – jrg Sep 09 '11 at 16:38
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Also, resetting compiz doesn't apply here, since Unity 2D uses metacity - Unity 3D is just a giant compiz plugin. – jrg Sep 09 '11 at 16:45
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unity --reset
will do the trick - I want the equivalent for Unity 2D. – jrg Sep 09 '11 at 18:49