MySQL - When Command column in Processlist shows "Prepare" or "execute"
The command status you refer to is pretty self explanatory:

1) The thread is preparing a statement, for example when the following:

PREPARE STATEMENT my_stmt FROM 'SELECT * FROM countries WHERE id = ?'; 


2) The thread ist executing a formerly prepared statement:

EXECUTE my_stmt;


You can also refer to the documentation: Thread Command Values