Handling Recovery of Disk Space in MySQL and MongoDB
InnoDB
I have mentioned how to shrink InnoDB tables and the System Tablespace (ibdata1) in the past

Mar 25, 2012 : Why does InnoDB store all databases in one file?
Apr 01, 2012 : Is innodb_file_per_table advisable?
Apr 15, 2012 : What happens when InnoDB hits its tablespace autoextend max?
Apr 15, 2013 : MySQL database drop insanely slow
Mar 31, 2014 : mysql directory grow to 246G after one query, which failed due to table is full

MyISAM
You could simply run for mydb.mytable
OPTIMIZE TABLE mydb.mytable;

which will shrunk a MyISAM table and recalculate the index statistics. To shrink all MyISAM tables, see my Jul 24, 2012 answer to MySQL: reducing ibdata file size for MyISAM tables
GIVE IT A TRY !!!