I went through a similar process recently trying to find a mapper that really covers all my scenarios as well. I've found ValueInjecter the best out of the automapper, emitmapper, and a few others on codeplex.
I choose ValueInjector because it's the most flexible of them all. I had a requirement to map from entity to viewmodel, and viewmodel back to entity, deep cloning where you have customer -> projects -> project, recursive situations like customer <-> project, and add/update/delete of children collections.
Out of the box ValueInjector doesn't support this, but it's framework is extensible enough to support this easily. You can see my extension point in this convention I posted on their discussion forum...
http://valueinjecter.codeplex.com/discussions/274484
