To rely on this apache-behaviour is a bad idea because it's a matter of its configuration if it shows you the files in a specific directory if no index is present. It's better to let the applet call a php-script on your server that gets you the list of files in simple ASCII-format and parse this one. You can access it via the Loaders getTextFile()-method. The script should look somehow like this little one:

<?
header("Content-Type: text/plain");
$d = dir(".");
while($entry = $d->read()){
echo($entry."\n");
}
$d->close();
?>

Hmm...this section of the jnlp should fix the problem: <nativelib href="lib/lwjgl-0.8/lwjgl.zip"/>
I don't know why it doesn't in your case. Please post your jnlp-file and try if my attempt works for you: http://www.jpct.net/webstart/demo4.jnlp
And try to empty your webstart-directory using the option webstart provides for this. Sometimes, it simply doesn't reload the jnlp the way it should.

An (unsigned) applet can only load resources from its origin, i.e. the server it came from. You usually can't access files on your local harddisc. That given, the behaviour you are getting is a bit strange...i would expect it to work with "textures" and to fail with "c:\....\textures" and not the other way round. It should work if you load the applet from the webserver and the textures too, but then you are having the problem to get the list of files from the server. That's what i tried to solve with my first reply.
Maybe signing the applet is a solution as it gives the applet full access to local (and remote) resources. The JDK contains everything you need to sign an applet. Your certifcate won't be a trusted one this way, but that's not a problem as long as your users are accepting it anyway.

You can set the codebase by using the codebase-attribute of the applet-tag. However, it's quite difficult to help you because i still don't fully understand the way in which you are accessing the applet. Maybe posting the corresponding html-page and how you call it would help? What exception do you get? Still a security exception or a simple file not found? Is the applet signed?

I still don't fully understand your problem. The applet is stored on the webserver, right? And accessed via a browser!? And the textures? Are they local on the users machine or on the webserver too?

Yes, you have to set the classpath so that it includes the jpct.jar (and the lwjgl.jar as well if you want to use OpenGL). This is needed for compiling and executing code that uses jPCT. You can set this temporally using the -cp directive like the example batch-files do or permanently by modifying your classpath-var.

Yes, you can serialize a world. It has been done by someone here in the forums. Just do a search for it. About writing the world out to XML: Well, the code to do this is there. but it's not active at the moment. I can add it to the next release if this would help.

The first call to moveCamera() moves the camera down into the middle of the virtual ellipsoid...or in other words: The ellipsoid collision detection for the camera takes the camera as the ellipsoid's center. But in this case, the ellipsoid is virtually below the camera (i.e. the player looks through his eyes, not his belly). To correct this, the camera is moved half way down, then collision detection is performed, then it's moved up again. If you remove the line you mentioned, the camera will be moved down and down and down...half the radius every frame and the ellipsoid collision detection can only avoid collisions but it can't push you out of existing ones reliable. That's the reason why you fall through the floor.
The other problem may be related to model complexity. The visibility list has a fixed size. Try to adjust this size (http://www.jpct.net/doc/com/threed/jpct/Config.html#maxPolysVisible) and see if it helps. You have to do this before instantiating your world.

Hope this helps.