The 3DRT Flexi Setup Utility v 0.8.0 and above supports adding hotspots:

Currently only the JavaScript hotspot type is supported. A JavaScript hotspot runs a custom function that you define. This way you can show e.g. a video or close-up image on hotspot click.

The Hotspot Id is your custom hotspot name.
The Hotsot title shows on mouse over. You can turn off this feature.
JavaScript function is the name of the function in the html page
JavaScript parameter is a custom parameter you can pass to the function

Before placing the hotspots, you must press “Initialize Images”. This will load all images from the folder you selected into the application.
Using the two arrows under the image you can switch to next/previus image.

You place the hotspt by draging and droping from the color rectangle area to the image. Once the hotspot is placed, you can use arrow keys on your keyboard to move it, or del key to delete it.
It is necessary to place (and adjust position) the hotspot in every image.
The “Cross” icon is only a placeholder. The actual hotspot shown in the player can be a custom movieclip, or one of the pre-defined shapes you can set in the Settigns->defaults tab:

If you choose a custom hotspot, you specify the class name of the Hotspot, as in the symbol properties windows in Adobe Flash (CS3 or above):
(The hotspot movieclip can be animated. You need to publish the .swf and replace the old one in the output folder with your customized version)

Currently, the 0.8.0 Setup Utility does not support specifying a custom hotspot class name for each hotspot. But you can specify it by editing the config.xml in your favourite text editor.
Example:
You can download and view an example here:
http://www.yofla.com/flash/3d-rotate/flexi/examples/example-hotspot/
Clicking on a hotspots launches a ShadowBox script which displays an image with Title.
This is an detail of the .xml file. The launchShadowbox function will be launched, with the parameter “detail.jpg|Title of the Hotspot Image”

This is the function which launches the shadowbox script:

If you have any questions when implementing hotspots into your presentation please let me know!