Scheduled optimization of tables in MySQL InnoDB
OPTIMIZE TABLE performs the following steps internally on a table (mydb.mytable)

CREATE TABLE mydb.mytablenew LIKE mydb.mytable;
INSERT INTO mydb.mytablenew SELECT * FROM mydb.mytable;
ALTER TABLE mydb.mytable RENAME mydb.mytablezap;
ALTER TABLE mydb.mytablenew RENAME mydb.mytable;
DROP TABLE mydb.mytablezap;


Since there is DDL involved, there is no way around queries taking a big performance hit during the operation. Additionally, not performing any optimization would be just as bad. 

What you need is to have MySQL Master/Master (aka Circular) Replication set up

You could then try this:

For Servers M1 and M2 and DB VIP pointing to M1

On M2, run the following

STOP SLAVE;
SET sql_log_bin = 0;
Perform OPTIMIZE TABLE or ALTER TABLE ... ENGINE=InnoDB on all InnoDB tables
START SLAVE;
Wait for replication to catch (Seconds_Behind_Master = 0)


The SET sql_log_bin = 0 would prevent the DDL commands from replicating over the Master.

Once those steps are complete, promote the Slave to Master, and demote the Master to Slave (can done by just moving your DB VIP from M1 to M2). You could perform this maintenance every day and production will not feel any effects with the exception of the Master Promotion and Slave Demotion.

You could create the script and run it on M2 like this:

echo "SET sql_log_bin = 0;" &gt; InnoDBCompression.sql
echo "STOP SLAVE;" &gt;&gt; InnoDBCompression.sql
mysql -u... -p... -AN -e"SELECT CONCAT('ALTER TABLE ',table_schema,'.',table_name,' ENGINE=InnoDB;') InnoDBCompressionSQL FROM information_schema.tables WHERE engine='InnoDB' ORDER BY (data_length+index_length)" &gt;&gt; InnoDBCompression.sql
echo "START SLAVE;" &gt;&gt; InnoDBCompression.sql
mysql -u... -p... -A &lt; InnoDBCompression.sql


From here, just wait for Seconds_Behind_Master to be 0 on M2, then move the DBVIP from M1 to M2. Now if you know the specific names of the tables you want optimized, you could adjust the query to fetch just those tables.

Give it a Try !!!

CAVEAT

Here is a fair warning: If you have innodb_file_per_table disbaled, every time you run OPTIMIZE TABLE or ALTER TABLE ... ENGINE=InnoDB; the ibdata1 file just grows. You would need to cleanup the InnoDB infrastructure to prevent ibdata1 from growing out of control.