Phew! Even the mighty power of google didn’t make this too easy..
Here are the steps I took to sign my applet…
- keytool -genkey -alias sig
- keytool -export -alias sig -rfc -file sig.x509
- jarsigner MyAppletjar sig
- Enter Passphrase for keystore: *******
- jarsigner -verify -verbose -certs MyApplet.jar
Strangely I’m still getting security exceptions (trying to connect to another server other than the one hosting the applet). I’m currently stumped 
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Perhaps the browser has cached an old, unsigned copy of the JAR?
I think that was probably the case, I’ve been having some wierd issues with IE seeming to lock applets in the cache. Killing all instances seems to fix it