With Integrator 3, there literally are a diverse number of possibilities as far as configuration and setup. Integrator 3 does provide SSO potential, but does so in a unique way.
With modules like JFusion and other SSO solutions, the user is authenticated one time and once logged in, the module or sso solution may attempt to 'handle' the login cookie itself. This may work fine, but there as often many updates to various applications, and different versions behave differently.
Integrator 3 takes a different approach. It with authenticate the user against any of the connections that it has (ie, Joomla,WHMCS, Wordpress) and if ONE of them authenticates, then it will proceed to log the user in based upon their email address by redirecting the user to each connection and permitting those connections to log the user in. This permits any third party plugins in Joomla or Wordpress to have the opportunity to act upon the logging in user in any way they may need to.
If a password is different in one of the connections, but the user has authenticated against another one, then (if set to) Integrator 3 will update the user password before sending them to the connection for log in. This only happens once the user has authenticated (meaning they have valid credentials) and I3 only works on a user with the same email address.
You mentioned you have multiple Joomla sites - are you wanting to connect those to another application, or simply to each other through their database? If you are just wanting to sync through the database a few different Joomla installs, then I would think jFusion would be the best method of going about this... I3 would need another application to tie into (though I haven't seen a situation with multiple Joomlas only... I'll have to test that out ;-)