MySQL still holding memory after I shut it down? I used this command to shutdown MySQL, however it seems the amount of free memory on my box has not changed? 

That seems to odd. 

/usr/local/webserver/mysql/bin/mysqladmin -u ${mysql_username} -p${mysql_password} -S /data0/mysql/mysql.sock shutdown

Does anyone know why the free memory might not change very much after unloading MySQL?
Memory management is a complex beast. If you are on a linux or similar platform, you might be seeing differences because of the page cache. This is a good writeup of what the page cache is.