Let me start off by saying that I really don't have a lot of experience with Lotus Notes. I was able to suffer through using the client for about a week before I finally begged the Notes admin to forward my mail to my Gmail account. As an email client, I personally found the Notes client application to be pretty much unusable.
But, my experience working with a company that uses Notes is that everything seems to be "in Notes." For example, ask the Human Resource department for information regarding hiring policies, and the answer comes back, "That's in Notes." If you need a copy of some recent financial data, guess where it is? That's right, it's "in Notes."
With the recent addition of Google Sites to the Google Apps suite, I think Lotus Notes can be effectively phased out of many organizations.
When I first wrote that, it seemed pretty obvious. The more I think about it, the more I realize that it's really a bold move. It's a major paradigm shift for most organizations. There is still a belief among many technology departments that data must be local to be useful. This is likely born from a fear that moving data somewhere else, in other words, outsourcing applications like messaging and document sharing, will mean a decreased importance for the group supporting the in-house versions of those applications.
Realistically, with Google offering a fully functional Intranet application, what's stopping you?