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Ubuntu Indicator Application

Unfortunately, system indicators cannot be moved in Ubuntu so you can't move the session indicator, the DateTime indicator and so on. Application Indicators are not easy to move either because you can't simply drag to reorder them, but you can specify their order in the Ubuntu Indicator Applet by editing a configuration file. Read on!

Update 7 May 2014: This was tested and works with Ubuntu 14.04! However, it only works with non-default AppIndicators, so you can't change the Power Manager indicator or the Network Applet indicator position.

1. To change Application Indicators position on the Unity panel, you must edit a file called "ordering-override.keyfile" which is located under /usr/share/indicator-application .

Since editing this file will change the settings for all users, you can copy it to ~/.local/share/indicators/application/ordering-override.keyfile and make the changes for your user only:
mkdir -p ~/.local/share/indicators/application
cp /usr/share/indicator-application/ordering-override.keyfile ~/.local/share/indicators/application/

2. Now open the file by running the following command in a terminal:
gedit ~/.local/share/indicators/application/ordering-override.keyfile

3. In this file you should see the existing rules for Application Indicators order on the panel. The first one is nm-applet and has a value of "1", meaning it will be the first Application Indicator to be displayed on the panel, from right to left.

For getting the Application Indicator ID, see Jiří Janoušek's comment below.

Using this as an example, you can add your own Application Indicators and specify their position by entering their name and a number like "clipit=7" which will make the ClipIt Application Indicator to show up as the 7th indicator on the panel (from right to left), if the other 6 indicators exist.

Important: If you want an indicator to show up as the last indicator on the panel (last indicator on the left), you must set a value to all indicators before it. You can't simply set a large value for a single indicator without setting a value for all indicators before it!

Here's an example in which I've set "indicator-weather" to show up as the first Application Indicator and "indicator-sysmonitor" as the last one (like in the screenshot above):
[Ordering Index Overrides]

4. Once you finish tweaking the Application Indicators order, save the file and log out (restarting Unity doesn't seem to work).

For Ubuntu 14.04, you can simply restart the Unity panel and it should work:
restart unity-panel-service

Note: I couldn't change the Dropbox Application Indicator position in the Indicator Applet because its PID is appended to the Dropbox indicator name, and the PID changes between session.
Info via AskUbuntu.