Custom my.cnf for a huge system with complex queries

Custom my.cnf for a huge system with complex queries

I am hosting a quite huge website, with millions of users visiting us weekly.
Currently we are using the file called "my-huge.cnf" as our configuration.
This is an example file from MySQL.
You can read more about the configuration files we use here:
http://dev.mysql.com/doc/refman/5.6/en/server-default-configuration-file.html
However, things are going a bit slow now, and we have upgraded our server,
and we got over 100 GB ram, multiple Xeon 8 cores cpu's. And we want to
customise the configuration. I am not asking for a ready configuration
file, I just want to know which values could I use with the specs, and
which of the options in the configuration should I change the value for?
Our tables are both of type InnoDB and MyISAM. We are considering
converting all to InnoDB.
Hope you understand my question here. Looking forward for an answer, so I
can learn more about this subject.