I am looking to create an integrated form of support to guide people to
explore complicated websites.  To achieve the software side of this, I've
been looking for some software that will allow me to
interface with the user's browser to pop up information 'tip' boxes.

Do you know of any software that exists (or you may have programmed)
that can help me with this approach?

I'm looking for some sort of software that sits on top and works with
the user's browser.  This software pops up 'tip' boxes depending on a)
what the user types into fields in a web page b) the sequence of links
they have clicked on when using the web site, c) some initial
questions they have answered at the outset (by filling in a form using
the software that sits on top of the browser) and d) which tip boxes
they have already seen and/or dismissed.

The closest thing I've found to any of this is a very buggy program
called RemoteIE (see
http://www.download.com/RemoteIE/3000-2366_4-10488956.html).  This
program lets you automatise interactions with IE by telling it which
URL to navigate to, which image or HTML elements of the page to click
on and which form fields to fill out.  I really need something that
works in reverse!

I'm looking for pointers to software that can be used to
achieve this (all of the above functionality, not just part of it).

See http://msdn.microsoft.com/library/default.asp?url=/library/en-us/dnwebgen/html/bho.asp
and more on http://msdn.microsoft.com/workshop/browser/overview/prog_browser_ovw_entry.asp