We have a similar problem at  Imperial College in our finance division.  On 
line access to the accounting system is via a  Java applet! At the moment, this 
is self-signed, and so they have the same problem as Jmol  has.  One presumes 
that anything to do with finance will have to be carefully scrutinised by 
lawyers, accountants, auditors.

The appropriate authorities here have promised to keep me in the loop.

Meanwhile, they gave me this page to look at 

http://www.sslshopper.com/cheap-code-signing-certificates.html

The four companies there all support  Java code signing.  The cheapest price 
for two years is  $360.  More importantly, all four are supported as 
“recognised” by the major  OS, and their browsers.  I would note that  I first 
got a code signing certificate around  1998 from Globalsign, so they have been 
around a long time.

Regarding who signs the certificate, my person here told me it is similar to eg 
registering a domain name.  An individual presents themselves as the 
“administrator” of the domain, but that does not necessarily mean that they are 
legally responsible for that domain.  I gather it is rather similar for code 
signing.  Thus the Financial  Java applet at  Imperial will bear the name of 
the prime administrative contact, without implying that this person is directly 
and legally responsible for all the financial transactions conducted using the 
applet.

I am more optimistic now that something sensible can be done quite quickly.

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