I know I did this the hard way. there is a command that you can issue that will convert them on the fly. what I did was mysqldump the database, reinstall mysql(because of other reasons), and then edit the dump so that the line that specified the engine reads "ENGINE=INNODB" instead of "ENGINE=MyISAM".Then I imported the dump.
I was getting annoyed that when listing my tables in phpmyadmin, it would show the list of tables in InnoDB (which is what i wanted), but then, when showing the summary at the bottom of the page, said "MyIsam". I easily got rid of it by adding "default-storage-engine=InnoDB" to my "my.cnf" file.