I know that in Doolin, McGann's Pub has B&B accomodations and excellent food & music, as well. Casey's in Baltimore, Co. Cork is a pub, hotel & restaurant.There is also a Casey's in Union Hall, Co. Cork, which is a Pub with lodging.
Those are the ones that I can recall at this moment. I am sure others on the forum will have other suggestions.
I used to have a website bookmarked for pubs with rooms but I just took a look and it is gone. You could check www.irelandhotels.com but would have to wade through a lot of other hotels and guesthouses.
Probably the best thing to do would be to post the locations you want to stay and we will tell you what we know.