Not getting into the whole which engine is the best debacle, since obviously, like most important questions in life the answer is: “It depends.”
In addition, most of what is written here can be used to convert from any engine to any engine, and thus answering any specific needs your might have.
I needed to convert MyISAM to InnoDB so here it is.
Without further ado…
As far as I know, there are two basic ways to accomplish this:
ALTER TABLE 'tablename' ENGINE = InnoDB
For each table in the database.
Obviously, these methods are ok when you are dealing with a few tables, however a while ago we had a client with a huge database with over 50 tables, so of course, a script was in place.