The main CS moment I can think of from season 3 is in 3.02 is when she goes to Chuck's place with all her stuff and tells him she's not going to Brown. Also, when he shows her his plans and she's all "I'm so proud of you!" on him.
Granted, I haven't watched anything post 3.16 (except for 3.20) so that can be a bit of a problem.
~CT