Dominating set problem
A quick google search revealed Experiments on Data Reduction for Optimal Domination in Networks. If you look at their tables they cite a number of data sets for which the actual dominating set is given. They also use a number of random graph generators and publish the average dominating set size for these. 

There's another paper from 2002: Experimental Analysis of Heuristic Algorithms for the Dominating Set Problem. I couldn't find an online copy, but I'm sure this paper also documents data sets and actual DS sizes.