I'm planning a long post on Israeli films, but in the meantime...
One of the best films dealing with the Six Day War is "Avanti Popolo", by Rafi Bukai, which is told from the perspective of two Egyptian soldiers trying to get back to the Suez Canal after the cease fire, and tag up with an Israeli patrol.
"Late Summer Blues" ("Blues le'hofesh ha'gadol"), by Renen Schorr, takes place during the War of Attrition, in 1970, and deals with a group of high school seniors between graduation and the army. One of my favorite Israeli films.
Amos Gitai's "Kippur" deals with the obvious, and tells his personal experiences from fighting on the Golan.
"Cup Final" ("G'mar Gavia") by Eran Riklis ("The Syrian Bride", "Lemon Tree") tells about two Israeli soldiers (Moshe Ivgi and Sharon Alexander) who are taken prisoner by Fatah fighters during the first Lebanon War in 1982.
All those films are excellent, and mostly give a complex viewing of the conflict.
As I said, I'm planning to post a detailed list of Israeli films from the past decade (most of the above films are from the 1980s and 90s) that I recommend. A preview (without comments): "Walk on Water", "The Syrian Bride", "Campfire", "Or", "The Band's Visit", "Meduzot", "Afula Express", "Broken Wings", "A Time of Favor", and whatever I'll think of. I'm just not sure on what board I should post it, but I'll let you know.