Depends on the constraints. Qt was around and mature for many years in 2006. Ruby on Rails had it's first release mid 2004. Django mid-2005.
Again it depends on the constrains, what you can "the best choice in 2006" is limping now. Meanwhile an app built in 2006 on Qt/RoR/Django would be on a platform that is currently still being considered for green field devt.
Without knowing all constraints I'd be willing to say that IE+applets was not the best choice in 2006, neither was: GWT, WebSphere or any of the MS GUI toolkits around in that year.
I'm still on the fence wrt Vaadin. It was not around in 2006, but soon after. Never used it, but it seems to still be actively maintained to this day.
But the lack of obviousness does not make IE+applets the best choice in 2006.
The timescale for a supplier to be in-business in order to prove their safety-critical credentials, the time it takes experienced developers to learn a language or framework and prove that it works, the time it takes to find, specify, build and deliver a project in these circles means you would be hard pushed to find anything that is less than 10 years old being used outside of startups.