I don't see why this feature requires unique names. As long as we have some unique way of identifying users (i.e., their ID), we're all set. And users don't even need to be aware of the ID's.
Here's how it would work:
When I post a comment, I am given three options to choose from (in the form of radio buttons):
- Don't notify me of any new comments
- Notify me only if a commenter tags me
- Notify me of all new comments.
(Note: You can change your selection at any time.)
Then users who post subsequent comments could tag any user of an existing comment using a drop-down checkbox list, like this
Notify [checkbox list \/] of my comment. This list would contain only the names of users who had agreed to allow someone to tag them, and perhaps it could include the first few words of the first comment that user left in case there happens to be two users with the same name/alias (and also just for general user friendliness, in that it makes it easier to match a name to a particular comment).
No one receives notifications (gets "tagged") who doesn't want them, and they can decide on a comment-by-comment basis. They should be able to change their selection at any time in case they change their mind.
Those who are willing to receive notifications are notified because someone was trying to get their attention, not just because someone said something random that didn't relate to their comment (unless of course they opted for full notification).
This is sort of a fleshed out version of Ian Elliot's comment & waveyλger's answer.
Just to clarify, when I say "notifications", I mean your little SO envelope icon turns red and you can click it to see your new comment responses. I don't mean it to imply email.