As a freelancer, what types of tasks do YOU charge for?

We all know working with our freelance clients can be a challenge at times, and sometimes time can be wasted, so I'm curious, how do you handle that when you're finalizing your invoice?

If you're learning something new for the job (say an API), do you charge for any of that time spent researching and learning it (having told the client at the beginning of the project)? What about time spent researching (I'm talking hours) things that the client could/should have given you in the specs?

Or do you just charge time spent coding/testing your changes?