Thanks Jeremy, the only issues I can see so far are where date formats are set as 0000-00-00 and 0000-00-00 00:00 by default instead of NULL (not XF databases)
I've found the following work-around for this on Stackoverflow by running the following to change them to NULL before changing the engine to INNODB....
update my_table set my_date_field=NULL where my_date_field<'0000-01-01'
...which worked on a test database