Be specific. Merely saying, "Hey, you did a great job in that meeting last week" may sound nice, but in practical terms, it is a fairly worthless remark. The problem is that the person you're talking to has no idea what he did that impressed you or how he made a difference. Give as much information as you can about why you're pleased and what effect the person's actions have had on the larger picture.
Be professional. It's better to tell someone how her good deeds or work affected you, rather than telling her what kind of person you think she is. You shouldn't presume to define someone (even in a flattering light), and personal assessments are just that -- personal. Instead of saying, "I appreciate what a thoughtful person you are," try saying, "I appreciate the way you took time to fill me in on that meeting I missed."