mysqldump seems to copy excessively
I think you are backing up all the Databases.You only need to backup those three databases.use mysqldump like:

mysqldump -uuser -ppassword --databases db_name1 db_name2 db_name3 &gt; Three_db_dump.sql


you can see various options of the mysqldump using      mysqldump --help.

In Case If you want to drop the 47 databases which you didn't want on new server If they all are having only MyISAM tables you can easily drop them.It will also reclaim the space.

If the databases have the InnoDB tables then you have to go with another process because only dropping the database doesn't recliam the InnoDB table space.For this follow the link

What is the best way to reduce the size of ibdata in mysql?