I want to make sure I cover all points related to my topic, so if I forgot anything let me know in the comments please.
I am discussing all the ways which Lotus causes confusion when you layer installations.
i.e Domino with Traveler on it causes http to go to the traveler download page, unless you change the reference is one example.
So with this in mind, the following items I have included(well outlined):
1) Mail Redirect
5) Virtual Websites/Multiple Domains
6) BES (more about config issues than http)
What else am I forgetting?