<p>Is it possible to sign only part of an applet?  Ie, have an applet that pops up no security warnings about being signed, but if some particular function is used (that requires privileges) then use the signed jar?</p>

<p>From what I can tell, some (perhaps most) browsers will pop up the warning for a signed applet even if you don't request privileges at all at execution time.  I'd rather avoid that if possible.</p>

I've been given the impression that Sun wants to discourage the creation of Applets and encourage the usage of Java Web Start.  I think this issue of signing applets is part of the problem.  See this documentation from Sun:
Java Web start FAQ
.
I haven't tried this, but could you segment the features that need signing into separate jars that only require permission checks when the user needs the functionality in those jars?