I agree that Portmarnock Links Hotel (attached to the Portmarnock Links course as opposed to the original Portmarnock Golf Club) is very nice but pricey. Unfortunately, you'll find Ireland to be more expensive the longer you stay in Dublin. The same goes with the Slieve Donard (next door to Royal County Down) and the Bushmills Inn (very close to Portrush). Both are very nice and very close to where you want to be... but expensive. I also agree with the earlier suggestion that you play County Down and Portrush at least twice each. So in that case, splurge and stay at the Slieve Donard and/or Bushmills Inn and play twice rather than spending too many nights in Dublin.
In Ballybunion, I'd suggest Irach ti Connor which is an elegant B&B (somewhat expensive again) BUT they can get you tee times at Ballybunion if you stay with them and are willing to play both the Old as well as the Cashen courses. Although I'd agree there's not much to do in Ballybunion, staying in town seems to afford you a better chance of getting tee times which can be hard to get otherwise.
In Lahinch, try the remodeled Lahinch Golf & Leisure Hotel which is in town and walkable to the course. Depending on the number of people in your group, you can put 3 or 4 of you in one of their "suites" quite reasonably and have much more room. I have also stayed at the Atlantic Hotel just around the corner. Fun, small bar downstairs and really good food. Also easily walkable to the course.
As for Waterville, I would say definitely play the course but avoid staying in the town. We stayed in the town a couple of years ago and regretted it. Somewhat dreary and very little to do.
Finally, you have to go stay in Kinsale and play Old Head. The course has been criticized in terms of its architecture but I think it's absolutely worth seeing and playing if you've never been before. Plus Kinsale is the most scenic town you'll find in Ireland. Stay at the Blindgate House which is a newer, modern B&B just a short walk from town or the Blue Haven in town on the main street. You won't regret adding Kinsale to your itinerary.