MySql - Clean ibdata1
Andreas got this answer first in terms of what to do. +1 for Andreas !!!

I would like clarify why that answer is the only way and how to do it.

By default ibdata1 normally houses four types of information


Table Data
Table Indexes
MVCC (Multiversioning Concurrency Control) Data
Table Metadata


Running OPTIMIZE TABLE against an InnoDB table stored ibdata1 will make things worse because here is what it does: 


Makes the table's data and indexes contiguous inside ibdata1
It makes ibdata1 grow because the contiguous data is appended to ibdata1


You can segregate Table Data and Table Indexes from ibdata1 and manage them independently using innodb_file_per_table. That way, only MVCC and Table MetaData would reside in ibdata1.

If you already use it, then you must have a high-write environment that stores lots of MVCC to support transaction isolation. Once the transactions holding the MVCC is done, the space is simply abandoned for re-use.

To shrink ibdata1 once and for all you must do the following:

STEP 01) MySQLDump all databases into a SQL text file (call it SQLData.sql)

STEP 02) Drop all databases (except mysql schema)

STEP 03) service mysql stop

STEP 04) Add the following lines to /etc/my.cnf

[mysqld]
innodb_file_per_table
innodb_flush_method=O_DIRECT
innodb_log_file_size=1G
innodb_buffer_pool_size=4G


Sidenote: Whatever your set for innodb_buffer_pool_size, make sure innodb_log_file_size is 25% of innodb_buffer_pool_size.

STEP 05) rm -f /var/lib/mysql/ibdata1 /var/lib/mysql/ib_logfile

At this point, there should only be the mysql schema in /var/lib/mysql

STEP 06) service mysql start

This will recreate ibdata1 at 10MB, ib_logfile0 and ib_logfile1 at 1G each

STEP 07) Reload SQLData.sql into mysql

ibdata1 will grow but only contain table metadata

Each InnoDB table will exist outside of ibdata1

Suppose you have an InnoDB table named mydb.mytable. If you go into /var/lib/mysql/mydb, you will see two files representing the table


mytable.frm (Storage Engine Header)
mytable.ibd (Home of Table Data and Table Indexes for mydb.mytable)


ibdata1 will never contain InnoDB data and Indexes anymore.

With the innodb_file_per_table option in /etc/my.cnf, you can run OPTIMIZE TABLE mydb.mytable; and the file /var/lib/mysql/mydb/mytable.ibd will actually shrink.

I would like to suggest a formula for you to query on sizing your InnoDB Buffer Pool from my post on What are the main differences between InnoDB and MyISAM?