McJoost, you have multiple WP sites on one domain. No matter how you look at it, having over a dozen WP installs is going to be slow. Even if you had Multisite, you’d be slowing down your server a lot. Also not all of your WP sites have caching, so that’s going to affect them.
That said, I see you have nextgen-gallery installed on many sites. There was a problem with version 2.0.23 which has been fixed by the developers. You need to make sure that you’ve upgraded that AND it’s been activated at least once, in order to clean out your SQL database properly.