I was in Dublin for five days before the tour. I think my favorite sight not on the tour was the National Archeological Museum. Other candidates would be the Chester Beatty Library, the state rooms at Dublin Castle, St. Patrick's and Christ Church Cathedrals, and the General Post Office. The Mary Gibbons tour to Newgrange was another highlight. Unfortunately I missed the student-led tour of Trinity College, partly because I expected to get something similar from the RS tour. But the RS tour focused on the Book of Kells and the old library, not the rest of the college.
In Belfast I'd say the Ulster Museum. Didn't have enough time to do much more there. The exhibit inside City Hall was interesting. I also appreciated the old church in Kinsale, near the center but not included on the tour. And I like boat rides, so those in Kinsale and Dingle were enjoyable.
I'd recommend the tour highly -- well organized, good amount of free time, absence of shopping stops, excellent guides, good hotels, plenty of room on the bus, interesting and well-informed fellow travelers. I haven't done a lot of organized tours but RS does a better job than anyone else I've tried. But if you prefer independent travel, even the best tour may not work for you.