There could be a check-box when you post a comment that says 'temporary'. It must be mandatory for you to ping someone in the comment to use this feature. You must also require a certain rep threshold to use this feature. Once posted, it will be visible to all that you have made a temporary comment.
When the other user who you have pinged sees the comment within a week's time, he has the authority to delete your comment. If the one-week deadline passes, it becomes an ordinary comment and you get a notification.
This can solve 2 major problems:
1. 'Thank you's - Many users like thanking other users, though SE policy does not recommend this. If you want to thank a user, you could just leave a temporary comment. Once he/she sees it, he can delete it, leaving no noise afterwards.
2. Clarifications - Often the OP is asked clarifications on his post. When the OP replies (and takes necessary action, such as editing the post), he could use a temporary comment. When the person who first asked the doubt sees this, he could delete both comments - his own as well as the OP's, leaving no mess afterwards.
I know that one could always flag comments to have mods delete them, but this is better since it reduces the work for the mods. Also people don't need to keep track of their past comments, since they have the assurance that the OP will see and delete the comments (or put another reply, which again notifies you).