The power of a blog that people actually read is amazing :) Within 10 minutes of that last post, I have a solution that solves pretty much all of the issues I was having with Command+Tab.
Witch (http://www.petermaurer.de/nasi.php?section=witch) looks to be exactly what I was looking for in terms of switching between windows rather than applications. It allows me to cycle through windows instead of applications and can order the items in terms of most recently used window instead of per-application (it’s default). It doesn’t show non visible windows like Quicksilver and Adium in the dock and it can zoom and minimise right from the Alt+Tab screen.
The only thing I can’t seem to do is make it replace Command+Tab. In the keyboard shortcuts system preferences panel, I can see the shortcut for cycle between windows Command+` but I can’t see one for cycle between applications, and when setting the shortcut for Witch when I try and press Command+Tab, of course it switches applications rather than setting the shortcut.
Thanks very much to Ton who left this recommendation in my comments.
There seems to be a small bug with Witch when you have it configured to cycle through windows in window use order. This works fine between windows in different applications but switching back and forth between the topmost two windows in the same application does not seem to select the correct window. I will e-mail the author and see if he can reproduce it.