Configuring MySQL (my.cnf) for MyISAM and InnoDB I want to convert some (not all) the MyISAM tables to InnoDB.


Current my.cnf 
Show engines output
Server has two 6-core Xeon processors (2 threads per core = 24 threads)


What would be the best configuration? (need to add InnoDB settings, because there are no InnoDB settings in my my.cnf).
You mentioned before you are running

MySQL 5.5.29
16 GB RAM

Here are some good settings to start with
innodb_buffer_pool_size=4G
innodb_buffer_pool_instance=2
innodb_read_io_threads=12
innodb_write_io_threads=12
innodb_io_capacity=300
innodb_log_file_size=128M

Don't do the conversion yet !!!
Put there settings in my.cnf, then do the following
service mysql stop
cd /var/lib/mysql
rm -f ibdata1 ib_logfile*
service mysql start

Now, you can do the conversion.
Give it a Try !!!
UPDATE 2013-05-10 10:44 EDT
Here are my past posts on tuning InnoDB for better CPU usage

May 26, 2011 : About single threaded versus multithreaded databases performance
Sep 12, 2011 : Possible to make MySQL use more than one core?
Sep 20, 2011 : Multi cores and MySQL Performance

Here are my past posts on tuning InnoDB

Feb 16, 2011 : How to safely change MySQL innodb variable &#39;innodb_log_file_size&#39;?
Apr 14, 2011 : What are the main differences between InnoDB and MyISAM?
Mar 25, 2012 : Why does InnoDB store all databases in one file?
Oct 22, 2012 : How large should be mysql innodb_buffer_pool_size?