Waterford

We spent two nights at the Granville Hotel in November and loved it. It's very old and historic but has been updated with modern finishes. It's right across the street from the water and in the heart of town. Breakfast was included; the highlight for me was their special oatmeal concoction that you mix with Bailey's--you know your in Ireland for sure!

I second that recommendation. The Granville was great and a convenient location as well. Also, the Medlieval Museum is not to be missed.

I stayed in the Waterford area a few times a few years ago when I was visiting for work. In Waterford I stayed at the Tower Hotel, it was fine, had free parking and within walking distance to all of the Waterford sites. A few coworkers stayed at Dooley's hotel and said it was good as well.
Since I was working on the other side of the River Suir, most of the time I stayed at the Fort Conan Hotel in Duncannon. It's a small family run hotel, more of a bed and breakfast feeling. They have great food, a bar, and the village has a couple of pubs, a fort, and a beach. I would highly recommend staying here, the owners made me feel like part of the family, but I also stayed for a couple of months.
To get to Waterford from there, it's a quick ferry ride (Passage East)...or a longer drive to a bridge in New Ross. Just depends on where you're wanting to be. The ferry runs later during the summer months and I think it's 12 euros for a round trip (8 for one way).