I just did it on our Moodle 2.0 test site and it looks like it went without issue. I just used the MySQL dump command (the one I use for DB backups), opened up the file in notepad and did a find/replace, replacing MyISAM with InnoDB. Then used the restore command to put it back in the server. Took less than 3 minutes.
Does anyone know if this causes any long term issues?