This is a thoughtful question. I felt the same way during my MA applications. The way I went about it was to first email the DGS telling them at least one reason why I chose another program. If they don't reply within a day (maybe they try to negotiate the offer?), I would go ahead and decline the official offer letter on the portal. I also thanked them for their enthusiasm. To the faculty members, I mentioned my interest in staying in touch (if you wish to). If they work in the exact field you're interested in, I would also ask if they'd consider being an external reader when I write the diss (I won't say this to someone who I haven't talked with in-depth about my work). To others, I just put it out there that I hope to see them at a conference or something. Hope this helps! And of course, mentioning that you're thinking about other people who're on the waitlist for that program is always a good practice.