Intercity Buses in Israel

There's an official list of routes on bus.co.il. But I would recommend using the Moovit app - it's very useful. You can look at different routes, and it gives you the different times and lists connections that you can make.

It also shouldn't go out of date as easily as other things - it should be updated fairly quickly if something changes.

If you are planning on doing a lot of bus travel in Israel, I would highly recommend that you get a Rav Kav. This allows you to get certain discounts on busses, and it's very easy to get one - you walk into the office, take a picture, and walk out. (It was free for me, although that may be because I'm a minor - not sure.)

In case that you have internet access, consider using standard google maps for planning routes. From my experience it works well in Israel, though the actual arrival times may be slightly off.

Where possible, I would recommend using the train, which is usually more predictable in terms of arrival times, and is also faster. Also note that you can get by train to the Ben-Gurion airport.

Keep in mind the unfortunate fact that public transportation does not operate during the weekend, starting with the entrance of SHABAT on Friday afternoon, and ending on Saturday evening.

Enjoy your trip!

Since I don't have enough reputation to comment I'll leave my answer here:

In order to get a RavKav you need to visit a Terminal station (that is the Tachana Merkazit) in most places that is the central bus station. In other places, offices are placed all around the city. In Jerusalem, there are various offices around the city to obtain a RavKav. You can also get an Anonymous RavKav from bus drivers (if they have). Cards cost 10 NIS (about $2.5 US). You will also need your Identification Card (in Israel that is a Teudat Zehut), or Passport for Foreigners). If you use your Passport and it has letters in the Passport number please be advised that there is no consistent way of storing these numbers - I believe they use "0" for a letter, but I have found that they have often not been able to find my number on file.

Currently (as of Oct 2018) you can simply add money to your card and use as needed), however, there are a few different options for those in the know - you can get a discounted rate a lot of times if you plan to return the same day. If you plan on just walking in your destination (i.e. no buses) you can get a further reduction. Israel is divided into zones and tariffs are designed accordingly - i.e. if you plan on traveling to the outer regions of Jerusalem or the Dan Regional Council (Tel Aviv) then you can get get a day pass, or monthly pass that covers all your transport needs in the city and to other cities within the greater Metropolitan area. For example: Say you want to travel to Western cities - such as Bet Shemesh, Beitar, Modiin, Modiin Elite, Gush etc. and return to Jerusalem, and use inner-city transport as well (the light rail, and Egged buses in Jerusalem proper) for a day. The pass will cost you: 26.50 NIS (about $6.6 US) a monthly pass is 300 NIS (about $100 US). If you're covering just the return trip, without travelling within the cities then it is 21.50 NIS ($7.1). Now without the discount to travel to any one of these destinations a single trip could cost you 14.50 NIS ($4.8 US). So the Day / Monthly pass could save you since you're getting all your rides free for the day in both your home location and destination! I always ask for a return pass if they exist.

Also you can get a monthly pass for your location and get all rides free for that month for a standard fare. For example in Bet Shemesh, you can get a month's worth of rides for 104 NIS ($34.60 US). There are other options and its worth it to look into it. Public transport in Israel is great, but you need to do your homework to save money.

As regards touring the Tourist destinations. It is worth it to go through a touring company. They have a speaker to explain it and you cover all the bases. To do it on your own means you need a car - the Tourist traps are not supplied by regular buses - sometimes they come at 8 am and 9am and again at 4:00 pm and 8:00 pm. If you're prepared to wait and do your own site-seeing you'll need to know Hebrew well. Also be aware that you could enter into an Arab Village rather easily both by car and on foot, and this requires special care especially if you have Israeli passports or Israeli stamps. Since your rental car will be Israeli, it might be pelted with stones and firebombs in these Arab villages. They're not safe and should be avoided.