<<Disclaimer: Verify this information before applying it to your situation.>>

Thanks to all who responded with very good information.  It sound like there are many options in Israel.  I have put together parts of all the responses and I hope this helps all who emailed that they were also planning to visit Israel too.

It is a very long post so I hope it comes through OK.
Burger places and cafe's have much bigger menus than they do here and can be a great casual option where lots of people can find a variety of things to eat. Black Bar 'n Burger and Aroma coffee (many locations across Israel) are good examples of this. In fact, I made it a habit of picking up their excellent pre-packaged rolls to have with me in case of emergency. Many non-Kosher restaurants where happen to have me use them in the restaurant and some of them even warmed them up for me in their ovens. There's an Aroma on every corner (kind of like Starbuck's with an expanded menu and good coffee). If you order a sandwich, they'll give you the filling separately, with the bun in the package, and then let you assemble it yourself to reduce the cross-contamination risk.

Natural Food stores (generically called - Beit Teva) have a great selection of gf foods. I had some fantastic pita (Brand - Bar-El) from the freezer section. Left it in our fridge and took it with us in zip lock bags for the day. There are also stacks of gf Israeli great cookies (Green Life were particularly good - watch for the delicious Moroccan cookies - finger like shapes) in these stores. They really are an Israeli thing and you'll see gluten versions in all the markets and bakeries.  

There's a lot of fresh food in Israeli - they don't do a lot of processed stuff - so it's pretty easy to eat in just about any restaurant. People are also reasonably aware of gf.

We had a ridiculously good meal at Mahane Yehuda (the restaurant, not the market). Hard to get a reservation, but a vibey, fun, fresh place that welcomes kids and adults. 

A word of caution: Israeli's use an Osem soup mix (a kind of bullion powder which is not gf) to flavour a lot of basic, seemingly gf starches (e.g. rice, lentils...). You might want to check about whether they use a bullion powder when asking about gf options.

There is a website that I found that lists some restaurants and brands of foods that are safe:
 http://www.israelinsideout.com/Gluten-Free-Products/

Other useful information:
-Health food stores, called Beit Teva, carry gluten free products -- best gf bread is Green Life
-The Israeli Celiac Society, http://www.celiac.org.il/ has information about restaurants that have gluten free menus and other useful information.
-On line service which delivers -- www.glutenfree.co.il  (Can also look at their products to verify gluten free)
-In Jerusalem, the 'machne yehuda' market has many health shops and a bakery which sells GF pita and other products. The Natural Choice Bakery  http://www.natural-choice.co.il/

In Jerusalem there are several shops with a large variety of gluten-free produce. One I recommend is Zmora Organi. They have three branches, the one nearest to us is on 1 Amatzia St., close to the German Colony - not cheap, but a good stock. Almost all health / natural food shops have at least a small selection of gluten-free products.
A cafe and patisserie called Ben Ami opened recently at 38 Emek Refaim St. in the German Colony, where they sell gluten-free cakes and biscuits.
Hummus at a restaurant, not the one bought at stores, and no pita, majadra (rice with lentils and onions), tahini are gluten free. What we call "shipudim", or kabobs would be suitable too, but not any minced meat.
As for gluten-free pizzas, my son says there are two in Jerusalem: Tito Bravo on 12 Shammai St. in the city center, and Pizza Hut at 1 Zalman Schneur St., in the Nayot neighborhood near the Botanical Gardens. The Pizza Hut is less accessible but apparently much better quality.
Ben-Ami on Emeq Refaim in Jerusalem, mentioned in a recent post, has a complete gluten free menu (for now, in Hebrew only--but i am sure they will translate it for you). the choices for appetizers, main course, and dessert were all extensive, and the food was very good and reasonable--especially for GF. The siblings of the owner, and the cook all have celiac. This is as good of a GF meal as i have had.
For those with celiac in Jerusalem, it is also worth knowing that you can eat many of the foods in the humus place Baba, also on Emeq Refaim. First go to the health food store across the street and buy some GF pitahs, which Baba will heat up for you to eat with their humus etc.

Fresco in Beth-Shemesh has good Italian dishes and a Gluten free menu.

There is a restaurant in Tel Aviv called Moses that has a GF menu on Rocthschild Street.  I had the burger on a gf bun with mashed potatoes.  They also had a dessert but I was full and didn't try it.  We ate alot of dinners down on the Pier, close to the Tel Aviv Hilton, and with all the fresh fish, and fresh food there, I had no problems, and using my restaurant cards, everyone was very helpful.

I am not sure if they are validated gluten-free, but this is what they used to declare:
1. Cafe, Veggie restaurant "MAZE", Achad Haam st, 51A, Tel Aviv
2. Hadson Restaurant, Habarzel 27, Tel Aviv
3. Tandouri, Indian Food, Mazkit 32, Herzelia
4. Marinado, Kibbutz Ein Gev
5. Giraff, Haifa, Sderot Hanasi 131, Haifa

*Please provide references to back up claims of a product being GF or not GF*
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