Aww Peter, still with this issue ?
It stopped working after I did some clean-up on Safari awhile back.
The cleaning and speeding up Safari really should not be the issue that created this this problem.
Try Safari in a other user or "Test" account, to create one:
Under the Blue Apple go > System Preferences /Accounts/ Login Options use the [+] to create one, for ease you could enter test in all the fields.
This will help to determine if there is an issue with your user account only or a system wide problem. It maybe a preference corruption or a 10.3.9 issue.
Look at this page on a fix that worked for this person when he & others would get this error this error
Java.lang.UnsatisfiedLinkError: getProxyConfigURL
http://www.tomrafteryit.net/javalangunsatisfiedlinkerror-getproxyconfigurl-error -on-os-x/
This was the result on my Applet test using same version os/safari & Java as yours.
http://www.student.oulu.fi/~sairwas/object-test/java/test4.html
I will try these link on java on my Tiger Powerbook & bet it will have better results.
Also check this out on how to configure the browser.
"your web browser is: Netscape Version: 5.0 (Macintosh; U; PPC Mac OS X; en) AppleWebKit/312.8 (KHTML, like Gecko) Safari/312.6 "
http://www.javatester.org/configuring.html
Good luck, hope you get it sorted out, please keep us posted; )
Eme