I would like to enable InnoDB on MySQL, for an application I want to install. Are there any dangers known in this (I'll back up first, just in case).
One of the dangers of InnoDB compared to MyISAM in MySQL is that InnoDB tables and databases take up space for information storage which they
never give back to the operating system, as this is the way InnoDB was designed. The only way to restore this space is with some manual fiddling provided you setup allows you (see below).
A possible way to limit this is to assign a separate InnoDB file per table instead of per database as is done per default by MySQL. I suggest you read-up on MySQL InnoDB in their manual.
So the possible caveat here is that even when you delete records from tables this free space will not be returned to the operating system and hence will not be available to other processes on the system and MySQL will 'eat' more and more of your hard drive.
Offcourse there are benefits to InnoDB as well. Are you sure you really need InnoDB?