Here's a small clip from The Assassination of Jesse James By The Coward Robert Ford that's a great example of thought process. In this shot Casey Affleck is coming to terms with the fact that he has to kill Jesse James (no its not a spoiler...its in the movie title haha) It's awesome how you can so easily see the stages of his thought process.
1st - he starts nervous/jittery, his head is moving more, licking his lips, eyes darting.
2nd - he slows down a bit, starts to concentrate, eyes look down thinking about what must be done.
3rd - he reaches his decision, eyes slowly look up in an almost villainous way and then he stands up.
Like your parents said when you were growing up "think before you act" so when you're animating make sure your characters are doing this too.