I've been using Lotus Notes for email for many years, first in the corporate environment and later when I was on my own. I use the Lotus Notes client stand alone for all my business email.
A function I use constantly is the Send and File function, which lets you save an out-going email to the folder you choose. So, for example, all my incoming and outgoing email related to a particular client is in one place. This is very much following the model of the hardcopy letter filing process, which I like. I want all correspondence for a client in the same place.
Except for a clunky add-on for Outlook, which may or may not be available if I upgrade Outlook, I haven't seen this function with any other email program. Many have the ability to indicate a reply, giving you sort of a thread, but it isn't the same.
It is difficult to get maintenance and upgrades for standalone Lotus Notes client. IBM isn't real interested in selling single licenses of this. In fact, the last few times I've asked for pricing I haven't gotten even a polite response. So I'd like to move to something more standard for the future.