At the heart of Sheldon's dislike of Penny is the fact that ... well, he simply does not like her. In the season 3 episode "The Gothowitz Deviation," Sheldon has to contend with the fact that, now that Penny is dating his roommate, Leonard (Johnny Galecki), she's going to be around the apartment much more frequently. Instead of getting over it and learning to get along with her, he comes up with a different, and much more, malicious plan.
When Leonard notices that Sheldon keeps giving Penny chocolates, he confronts his roommate about his unusually friendly behavior. It's then that Sheldon reveals what he's up to: He's attempting to train her to stop doing things that annoy him using positive reinforcement. Of course, Sheldon being Sheldon, he has a scientific explanation, saying, "I decided to employ operant conditioning techniques, building on the work of Thorndike and B.F. Skinner. By this time next week, I believe I can have her jumping out of a pool, balancing a beach ball on her nose."
Trying to train an adult person like a circus seal is a pretty despicable thing to do. While we're on the topic, Leonard probably should have made Sheldon cut it out, or at least told Penny what was going on. On the other hand, the fact that Sheldon is figuring out ways to deal with Penny being around the apartment at all is a step forward in their relationship. After all, at one point, he banned Penny from coming into the apartment altogether.
