discuss.answer
Yes, and I believe you can even convert the site_content table as well with more recent releases of MySQL which support full-text searches. Even without that support in recent releases of MySQL, most everything should work on InnoDB, unless you use extras that make use of the full-text index.
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There are some problems when installing packages, they could create database tables using MyISAM, witch in our case broke the mirroring of that database. (we use 2 separate servers to balance the load)