These are really only a very small subset of Israeli military action that can / has been classified as war crimes.

Israel attacks UNITED NATIONS compound – Qana, Lebanon

18 April 1996 – A UN compound sheltering more than 800 civilians came under a sustained Israeli attack, killing 106 people. At this time, Israel was occupying South Lebanon and Lebanese guerilla forces were launching rockets on Northern Israel. Israel claims it was responding this rocket fire when it attacked the UN compound.

An Investigation by UN concluded that: “it is unlikely that the shelling of the United Nations compound was the result of gross technical and/or procedural errors.”

Israel attacks UNITED NATIONS school

2004 -  during Operation Days of Penitence in the Gaza Strip, seven civilians were killed by tank fire at an UNRWA school in Jabalya.

Israel attacks UNITED NATIONS compound – Qana, Lebanon

30 July 2006 -

Israel attack MERCY VESSEL in international waters

As the latest US-Israeli assault on Gaza began, a small boat, the Dignity, was on its way from Cyprus to Gaza.  The doctors and human rights activists aboard intended to violate Israel's criminal blockade and to bring medical supplies to the trapped population.  The ship was intercepted in international waters by Israeli naval vessels, which rammed it severely, almost sinking it, though it managed to limp to Lebanon.  Israel issued the routine lies, refuted by the journalists and passengers aboard, including CNN correspondent Karl Penhaul and former US representative and Green Party presidential candidate Cynthia McKinney.  That is a serious crime -- much worse, for example, than hijacking boats off the coast of Somalia.  It passed with little notice. 
http://www.zcommunications.org/znet/viewArticle/20316

Israel attacks a UNITED NATIONS schools - Gaza

7 January 2009- Israeli strikes killed at least 43 people taking refuge inside a UN school (al-Fakhoura) run by the UN agency for Palestinian refugees, Unrwa, in the northern town of Jabaliya in the Gaza Strip.

The night before, the United Nations said, three Palestinian men were killed in another Israeli attack on a small co-education United Nations school for refugees in Gaza City.

Israel attacks a UNITED NATIONS Compound - Gaza

15 January 2009 - Israeli artillery shells struck the U.N. headquarters in the Gaza Strip, setting a food warehouse ablaze destroying thousands of pounds of food and other aid intended for Gaza's beleaguered citizens. The U.N. compound, made up of workshops and warehouses as well as offices, was struck about a half-dozen times over a roughly two-hour period while more than 700 civilians were sheltering there.

http://news.yahoo.com/s/ap/20090115/ap_on_re_mi_ea/ml_israel_palestinians

The senior UN official in Gaza, John Ging, meanwhile described as "total nonsense" and "typical misinformation" claims by Israel that militants had fired from a UN compound shelled by Israel on Thursday.

http://news.bbc.co.uk/2/hi/middle_east/7834255.stm

Ging said the U.N. had warned the Israeli military that the compound was in peril from shelling that had begun overnight. U.N. officials say they have provided Israel with GPS coordinates of all U.N. installations in Gaza to prevent such attacks.

http://news.yahoo.com/s/ap/20090115/ap_on_re_mi_ea/ml_israel_palestinians