I think this has been mentioned before already, but just not to forget:
make a backup
make another backup
make more backups ...
jOpenSim takes basically the same database structure in 3.x like in 2.5.x. So if you have all tables in your Joomla database starting with #__opensim_ (replace #__ with your DB prefix) from your previous 2.5.x, jOpenSim will take care for all changes during installation/upgrading.
InnoDB vs MyISAM
Depending on the age of your previous jOpenSim installation, it could be that you still have tables with MyISAM instead of InnoDB. jOpenSim will intentionally NOT convert the tables for you! And in most cases it does not really make much difference (yet). The only tables that require InnoDB since jOpenSim v 0.3.x are all tables starting with #__opensim_money. On some grids, these tables may contain a LOT of data and converting it automatically could result in a timeout due to max_execution_time of your server settings and end up with a failure in installing/upgrading jOpenSim. This why jOpenSim does this not automatically for you, but it will check and give you a warning message after installation.