A couple of years ago Ludovico Magnocavallo tackled the issue of bulk conversion of MySQL tables from MyISAM to InnoDB with an elegant bash snippet.
for t in $(mysql –batch –column-names=false -e “show tables” mydbname); do
mysql -e “alter table $t type=InnoDB” mydbname;
done
mysql -e “alter table $t type=InnoDB” mydbname;
done
The original post also suggests using grep to limit the scope of the conversion to just a few tables.
(It seems that now Google *does* yield practical answers to this question ;-)