Cool, so essentially putting together traning, user guides, educational material that's accessed in a web browser (even if locally or local area network) and in that case I'd look for Flash. Not the tool from Adobe, just the output format. If you want a good 2D authoring tool for some of that, Wink from debugmode.com - if you prefer Adobe stuff look at Captivate

I'll check if AnimeSTudio has html output with their Flash render that might include hot clickable zones. It does allow in the Pro version to load 3D objects. They have had 3D layers years before Adobe added it to Photoshop CS3.  They already had 3D layers back in the days of when it was called MoHo

 

Now if you want to make the clickable 3D zones be inside the 3D view, the 3D model, such as that you can click the spark plug of a V6 no matter from which angle in 3D you're looking at it, allowing the user to interactively view and rotate and  navigfate into the scene and yet still see the clickable and use the clickable items, or such as an architectural walkthrough where the door is clickable so you can open it and transition into the next room,... That's when you'll need a full 3D pipeline, not just Flash and video inside a Flash project with 3D hotzones. In that case, if you want a true 3D interface, don't look at vrml. Look for a Gamedev system. Game dev systems are all making it more and more affordable and attractive, some without programing skills required, to make 3D interfaces. A house with clickable doors is essentially a 3D interface: a bunch of polygons, and afew of them are hot and clickable to link you to another bunch of polygons.

 

www.thebest3d.com/gamedev  has a list of gamedev solutyions, some I'd recommend are  GarageGames (now at yoyogames), they're about to release a new version with target for mobiles. Believe me, your solution must include iOS if you want it to have a future beyond the next budget cycle. iPads are not just here to stay, they're here to dominate. And I don't have one either. Other tablets, they run Android and Windows 7 soon WIndows8, that interface is totallt tablet centric. I just bought a monster laptop yesterday, they couldn't believe there was still someone interested in buying laptops on the planet lol. There are so many more users now consuming learning material, and attending webinars with iPhone, iPad, tablets... companies that deliver such content like webex and Go2meeting etc... they all have released viewers/players for the tablets, and I see my audiences use those platforms. Mobility is key. The ability to learn on the go is a huge plus.  EVen if you can't watch a video while driving, the audio can be absorbed while commuting to/from home...One of the many hats I wear is instructional designer at Eset, working with Video, doing translations.... here's one I did in a hurry in Captivate http://go.eset.com/us/resources/training/ess5_installation_fr/player.html

 

Have fun, wish I could be on your team for this one :-)