Following are some website recommendations that have been mentioned frequently on Janglo. 

Egged:

You can call Egged at *2800 and ask for information about exactly how to get rom one place in the city to another. They will tell you the times of the buses at each station you need, how many buses, the direct route, and more.

You can also look at their website at www.egged.co.il/ENG to find out how to get from Jerusalem to other cities. Note that Egged doesn't service every city, so you might need to contact another bus company. 

Municipal portal:

A portal for all municipal services in the country. www.toshav.co.il/ 

Kupot Gemel:

Here's an excellent website (in Hebrew) put out by Misrad Ha'Otzar which ets you compare the yields of up to 4 different kupot gemel at a time:

gemelnet.mof.gov.il/Tsuot/UI/DafMakdim.aspx