Bob is probably more knowledgeable than me, but this is how I see things:

If you have the HTML4 doctype in the header, the browsers will interpret as 
such. No problem 
with <applet>. After all, this tag is already deprecated in 4.01, but the 
browsers respect it.

http://www.w3.org/TR/html401/struct/objects.html#h-13.4
says 
"APPLET is deprecated (with all its attributes) in favor of OBJECT."

Only pages with the HTML5 doctype (which, BTW, is absolutely simple: <!DOCTYPE 
HTML> 
) may produce the reject --and I bet that the browsers  will still render it, 
since they tend to be 
conservative and forgiving.
Maybe pages without any header will be interpreted by browsers as HTML5 by 
default in the 
future and so break.

I don't think it is a question of pages stop working, but rather of start 
coding better for the 
future.

And Jmol.js takes care of inserting the proper tag (currently, <object> if the 
detected browser 
supports it). <applet> remains only in pages coded manually.


On another line, my former comment in this thread was trying to decide whether 
we must 
remove the pages from the website that give examples that use applet tag. Or 
maybe rewrite 
it to use object tags?
That's mainly  http://jmol.sourceforge.net/scripting/



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