I had all my tables in myISAM but the table level locking was starting to kill me when I had long running update jobs. I converted my primary tables over to InnoDB and now m
My guess is that you probably haven't configured your InnoDB settings beyond the defaults. You should do a quick google for setting up your InnoDB options.
The one that caused me the most noticeable performance issues out of the box was innodb_buffer_pool_size. This should be set to 50-80% of your machine's memory. By default it's often only a few MB. Crank it way up, and you should see a noticeable performance increase.
Also take a look at innodb_additional_mem_pool_size.
Start here, but also google around for "innodb performance tuning".