Depends on the specific boat, style and how big, but basically on cruisers:
I/O generally are more economical and faster. Usually have more room in the engine room too. But I/O have a lot of maintenance hanging out the back end which is pretty expensive if you have to do repairs.
Inboards usually handle much better around the dock (at slow speeds). Less maintenance and less hanging in the water to corrode/dent/damage. Obviously, can't raise them up though....
Boils down to personal preference. If it were me, I'd get inboards on anything over 32'.