This link will probably not work, but it can be found archived in full if you got a website. Upon the return of some Flotilla sailors to Istanbul, this Dutch paper interviewed those present (and willing) to speak about their treatment while imprisoned by Israel. The list comes down to this, and whereever you draw the line, there are some grave offenses in here.
Intervering on international waters
There were clear signs of the Israeli army blocking any radio communication from the boats to each other, as well as to any mainland stations. Instead they would hear Britney Spears' Oops... I Did It Again. This is problematic for a number of reasons, most of all that any signals of distress would not reach harbor institutions that could send help, but also because this happened in international waters where no state has jurisdiction.
Systemic (psychological) abuse
Will list this because it's a lot.
Shooting rubber bullets at unarmed civilians
Dousing people in water and forcing them to sleep (semi)outdoors
Tasering unarmed civilians (sometimes while they were soaked)
Forcibly removing hijabs and other head coverings
Keeping people tie-wrapped at the wrists for over 24 hours
Forcing people in uncomfortable positions (such as kneeling) for over 24 hours
Keeping people from sleep
Providing little food and water
All this not by individuals, but by groups or militia men, in full view and knowledge of any higher ranking figure. One of the sailors said how their abuse was put on as a spectacle for all to watch, but those beating them were careful enough not to hit anyone in a visible spot (such as the face). He says that a majority of the Flotilla sustained broken ribs.
This man is one of two journalists aboard the Flotilla. They were there to document the (attempted) journey to Gaza from their departure in Barcelona. From the start, it was agreed with the network they were doing this for that any files would be uploaded as to keep them safe from confiscation/destruction, and to throw their devices overboard if they were to be taken by the Israeli forces. These files have been saved, and if the network here goes forward in putting them together for a broadcast, it could mean a lot to at least have something on the journey out there for all to see.
All the activists stated the gravity and severity of their treatment while imprisoned, but all underline that this is a fraction of what Palestinians (risk to) experience on the daily. It's hoping that this might finally be a wake-up call, or that this at least puts a heavy dent in the Israeli PR machine.