I developer a BIG system OPEN SOURCE with Yii http://www.magnusbilling.com
In this system there is a big table that can have more than 3 millions, and about 3 or more new inserts per seconds.
Actually I use InnoDB, but is the better option?
3 million is not big InnoDb is one of the best open source engine out there, there are commercial engines e.g. percona XtraDB
depending on the workload there are other options contact me if you would like to discuss this further.