Why do you think Holden cries before he leaves Pency?

There are many explanations as to why Holden cries before leaving Pency. One explanation would be that he was sad at the fact that he had been kicked out of yet another school. Another explanation would be that he knew he would have to go to another school, he knew he wouldn't be able to do so well, and he knew that he would be kicked out again. Yet another explanation would be that he felt lonely, he had almost no friends at Pency, he had no family members he cared about. He pretty much didn't have anyone to talk to about his troubles and insecurities. It is also possible that he was thinking of all of these things while crying.
Holden is a person who likes to look at all the negative traits of a person, he shares his problems with no one, underestimates himself at every point, puts on a "tough guy" mask, and does not care about others. Looking at his traits the most obvious answer would be that he was tired of the process he had to go through almost every year. Getting into a new school, trying to fit in with everyone else, failing at academics, getting kicked out of the school. He knew that he would have to go through the process again and that fact made him sad.
Allie was a very intelligent kid, Phoebe is also very intelligent, and D.B. is also intelligent. Holden is the only one in the family who did not shine at academics. It makes him feel different and lonely. Pency is an example of his failure and therefore when he looks at the building the burden of being a disappointment makes him really sad and therefore he cries.
Holden is a very lonely person, he has no friends to share his feelings with. He relates his memories and feelings with objects such as Allie's glove, his hat, the typewriter, etc. Since he has no one to talk to he writes down his memories in the form of literature. While leaving the school he knows that he will be lonely again. He had become friends with Ackley and Stradlater but he was axed and was alone once again. The thought that he would have to leave the school and start anew at another school made him sad.
Holden was probably thinking of about one the three things above when he started crying. All the reasons make sense but one was probably enough to make him cry.