I just upgraded to Mavericks 10.9.3 from Mountain Lion and the emoticons / emoji are quite small in Messages. Sometimes I can't even tell the difference between one and another emoji.
When I open the emoji panel they are bigger, at the size I was accustomed to in 10.8. You can see in the picture the size they appear in a message, as compared to the panel.
I've tried making the font bigger in Message's preferences, but the emoji won't change their size either.