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: it. Can I just confirm I understand the difference between the
: three email addresses:
: Maillist: the incoming address - effectively an email to
: contact the admin / moderators, etc.?
: Notification: the address outgoing forum messages comes
: from, notification for users of replies, etc.? This is quite
: often a non-replyable address, is it not?
: ReplyTo: this is intuitive.

Basically yes.
However, check it out with a couple of testposts on your forum using different addresses for initial post and responses.
Usage depends a bit on how exactly the other features are set.

: However, I've seen WebBBS forums which seem to have an address
: like so: http://forums.bungie.org/story/ which I'd like to
: replicate if possible. I know WebBBS and this aren't the same,
: but is it possible?

Yes. But that's nothing related to the forum software but depends on how your server is configured. If you're on Apache, then you can try to adjust server configs via .htaccess. The directive you're looking for is DirectoryIndex:
http://httpd.apache.org/docs/2.0/mod/mod_dir.html

: My server can run both .pl and .cgi - is
: there a benefit to choosing one over the other?

Unimportant from a technical point of view.

: Also, the setup guides mention moving the /bbs and /lib folders to
: a location which is not web-accessible. How do I achieve this -
: using .htaccess?

Move the /bbs and /lib folders to a place "higher" than your public_html or htdocs or www folder used for the web documents.
Depends if your host allows to set up your server in such a way. Logging in via FTP should give you all information required.
If that's not possible, then .htaccess is your only options - if it works as expected on your server.
Can't be more specific without viewing debug output myself.

: However, my domain
: is intended to be a sort of anonymous / secret project so I'd
: rather not reveal it publicly.

Secret project on the internet? Good luck

.... you may check your server logfiles and probably already find bots hitting your site.
.... and for a "secret project", how do you keep your visitors from spreading links to your site? Without visitors a forum wouldn't make sense, so likely you have visitors.

... if you want to protect your site, then password protect it. However, then it would be unimportant to mention your URLs for the time of setup things.

my 2cts.

Rainer