Although InnoDB has some benefits over MyISAM, at least on the paper, I have completely come back from using it after a database corruption, at least for all my mutiple website developements on localhost.
With MyISAM, when you want to backup the database of a site, you simply copy the mysql/data/<your-website> folder in which are the .MYD, .MYD, .frm files. The copy-paste method works for restoring databases.
With InnoDB, the databases of your miscellaneous websites are all linked together into a very few files.
In some cases of database corruption, file copy-paste operations usually don't work and will even corrupt your database.
You can play during whole days, weeks or more trying to solve database errors and restoring your database, and be unsuccessful at the end. This arrived to me few years ago. Never more.
For experts, I think it is possible to configure InnoDB differently, for the average user, it has a complexity of which he is unaware.
Of course, InnoDB is likely more stable than few years ago and database recovery tools may have improved as well.
(They were really few available when the crash occured for me.)
Of course it is also still possible to export SQL dumps to backup databases.
An InnoDB expert would also probably know what to do when the database crashes.
But as for myself, although InnoDB is in use on some webhosts, I strongly prefer staying with MyISAM for my local projects.
