Among the various statements of outrage targeted at Israel, many point to Israel's confronting the "flotilla" ships in international waters as a sign of Israel's guilt.

I direct your attention to the San Remo Manual on International Law Applicable to Armed Conflicts at Sea. Specifically, paragraph 67-68:

67. Merchant vessels flying the flag of neutral States may not be attacked unless they:

(a) are believed on reasonable grounds to be carrying contraband or breaching a blockade, and after prior warning they intentionally and clearly refuse to stop, or intentionally and clearly resist visit, search or capture;
(b) engage in belligerent acts on behalf of the enemy;<
(c) act as auxiliaries to the enemy s armed forces;
(d) are incorporated into or assist the enemy s intelligence system;
(e) sail under convoy of enemy warships or military aircraft; or
(f) otherwise make an effective contribution to the enemy s military action, e.g., by carrying military materials, and it is not feasible for the attacking forces to first place passengers and crew in a place of safety. Unless circumstances do not permit, they are to be given a warning, so that they can re-route, off-load, or take other precautions.

So these were ostensibly merchant vessels who were flying the flags of neutral states (since Turkey and Greece have not declared that they officially side with Hamas in their war for Israel's destruction). However, there was definitely reasonable grounds to believe that they were carrying contraband and breaching a blockade (since that was there very public, stated intention). After receiving prior warning (see this YouTube video) they intentionally refused to stop (I heard that they just radioed back curses in Arabic and English), and they quite clearly resisted visit, search or capture.

So this would have legitimized an attack by Israel on the vessels themselves, pursuant to paragraphs 38-46 of the treaty - note: Israel did not attack the vessels, they merely sought to prevent them from breaching the naval blockade of Gaza and redirect them to the Port of Ashdod where their supposed humanitarian supplies would then be rerouted to Gaza, along with the rest of the aid that goes in every day to not-so-starved Gaza.

With regards to Neutral waters:

14. Neutral waters consist of the internal waters, territorial sea, and, where applicable, the archipelagic waters, of neutral States. Neutral airspace consists of the airspace over neutral waters and the land territory of neutral States.

So Neutral waters would be waters of a neutral state. This is not a valid description of the location of the confrontation between Israel and the boats.

So now that we have established that this did not take place in Neutral waters, look at the following:

118. In exercising their legal rights in an international armed conflict at sea, belligerent warships and military aircraft have a right to visit and search merchant vessels outside neutral waters where there are reasonable grounds for suspecting that they are subject to capture.

119. As an alternative to visit and search, a neutral merchant vessel may, with its consent, be diverted from its declared destination.

So according to this, since this did not take place in Neutral waters, and there were reasonable ground for suspecting that the ships are subject to capture (see analysis of paragraph 67, above), Israel was fully within its rights to go so far as to capture the vessels in question (they did offer to divert to Ashdod, which was rejected by the captains of said vessels).

The material above makes it clear (at least in my opinion) that Israels actions, if not justified, are at least not immediately guilty in both their intent and location.

And international law itself is always a tricky topic - after all, if a country does not sign on to a treaty governing any specific agreement, how can one say that their violation of said treaty would be a violation of International Law? International Law defined by any treaty or agreement only applies to countries who agree to the precepts of said treaty or agreement. Which makes it even more difficult to indict Israel on the basis of interpretations of the San Remo Manual, being that Israel (and Turkey and Greece) is not even a signatory. Similarly, Israel is not a signatory of the United Nations Convention on the Law of the Sea, which seems to take a harsher view of these types of actions in International waters (thus a violation of the precepts of this UN convention by Israel would not be in violation of International law, as Israel never signed on the dotted line).

Israel's position: See the official response by the Israel Ministry of Foreign Affairs (seed). Most pertinent for our case:

7. Under international maritime law, when a maritime blockade is in effect, no boats can enter the blockaded area. That includes both civilian and enemy vessels.

8. A state may take action to enforce a blockade. Any vessel that violates or attempts to violate a maritime blockade may be captured or even attacked under international law. The US Commander's Handbook on the Law of Naval Operations sets forth that a vessel is considered to be in attempt to breach a blockade from the time the vessel leaves its port with the intention of evading the blockade.

9. Here we should note that the protesters indicated their clear intention to violate the blockade by means of written and oral statements. Moreover, the route of these vessels indicated their clear intention to violate the blockade in violation of international law.

10. Given the protesters explicit intention to violate the naval blockade, Israel exercised its right under international law to enforce the blockade. It should be noted that prior to undertaking enforcement measures, explicit warnings were relayed directly to the captains of the vessels, expressing Israel's intent to exercise its right to enforce the blockade.