I agree with Matt on Old Head and Doonbeg. I think a lot of the problem that Doonbeg has is the whole non-Irish feel. The place feels more like Kohler than Ireland and it causes people to look down on it a lot. That and a few uninteresting holes in the middle of the round.
I've played 39 of the top 100 listed here over the last 10 years and have some opinions on where things lie. Narin & Portnoo is way too far down IMO as it has some great holes. Portmarnock is too high as well. I find all of the courses at Killarney to be absolutely boring and the group I go with agrees. I'm not sure where they fall but, again, IMO they are way too high on the list. Honestly I've played 13 of the top 15 and 25 of the top 30 listed and would move several around based on my opinions. I do love RCD at #1 though as it is simply wonderful.
Just to give you a feel for what people think that are a bit less obsessed with the technical details think I have been on a 2-3 week trip to play in Ireland 9 of the last 11 years. The group I go with has about 5 or 6 core members that almost always go (people like me), another handful that go a few years here and there and then some first timers. We usually rotate NW, SW and then Dublin/Northern Ireland every year to keep some variety going. I can tell you without a doubt that Old Head is by far the most popular course we play. This is by a wide margin. In an informal, anecdotal poll I would say that I've asked 50 first time people on the trip over the years what their favorite course we played was and Old Head is 50 for 50. The second favorite course will be all over the map. My point is that Old Head is good enough golf that when you combine it with the views that people just simply love it. I would be hard pressed to find a more beautiful spot to walk around for 4 hours than Old Head when the sun is shining so I can certainly see it. That said, Enniscrone is probably my favorite place to play on the list. It isn't the best course but is my favorite place to play.
Generically I would say our group kinda puts this out as a top 10
1. Old Head
2. Enniscrone (we have been there many times and have a great relationship with the place)
3. Royal County Down
4. Ballybunion Old
5. Lahinch
6. Ballyliffin-Glasheedy
7. Royal Portrush
8. Tralee
9. Waterville
10. Narin & Portnoo (we played it as a group for the first time in 2009 and everyone agreed that we needed to come back)
Co. Sligo is interesting as many of our group think it is horrible (I admit I'm one) but one person would probably put it first or second. He organizes the trip so we have been there 4 or 5 times but he's been getting so hammered on it by the rest of the group that he said he wouldn't go back next time.