While we originally thought a week in Jerusalem was excessive, we're glad for the extra days we had to explore the city because we never intended to visit right in the middle of the Jewish holidays - Yom Kippur and Sukkot - as well as the Sabbath, where everything literally shuts down. Although it was nice to have a few "forced" days of rest right alongside the locals celebrating their holidays...the lack of public transportation and closed businesses made us think of other nice-to-have-known tips for visiting Jerusalem.
APARTMENT
We rented an apartment in the German Colony area called Bak'a in West Jerusalem. They raised the prices for the holidays, but it was still about half the cost of getting a hotel room in West Jerusalem. We chose not to stay within the Old City because there isn't much to do after hours. Although cheaper, we didn't even consider East Jerusalem (the Muslim side) because the nightlife and shopping were on the west side, plus we heard that the airport shuttles do not like to go to the east side. When we took a public bus over to Mount of Olives on the east side, we got a good look at the neighborhoods and we were very glad we didn't book a room in East Jerusalem.
As for choosing the Bak'a neighborhood, we read that it was a quiet area with lots of restaurants and stores, and only about a 30 minute walk to the Old City and the city center. We were very happy with the location, especially when we found ourselves stranded when the buses stopped operating for the holidays and the Sabbath, and we had to walk home! And, although most things are written in Hebrew, we've never heard so much American English being spoken by people in this neighborhood who did not look like tourists, rather residents.
AIRPORT AND SHUTTLE
With our weird flight schedules, we were very worried about transportation to and from the rental apartment in the middle of the night. Nesher Sherut (shared shuttle vans) to the rescue! They operate 24 hours a day, 7 days a week. We easily located them outside of baggage claim, and after 62 shekels per person and an hour later, we were being dropped off in front of our apartment. For our return transportation, we stopped by the Nesher office at 23 Ben-Yehuda Street (a popular pedestrian road) and made our reservations for a 3 am pick-up. They showed up early, picked up a few more people along the way, and we were at the airport by 4 am. They asked for an Israeli phone number when making the reservation, so we gave the phone number of our apartment host. If you don't have access to an Israeli number, this could be a problem. Also, remember that they may or may not service any East Jerusalem addresses, and we aren't certain of any similar Arab shuttle services so taxi would be the way to go.
Upon arrival, customs and immigration through Ben Gurion Airport was a breeze. There was a lot more scrutiny upon leaving Israel, but the airport personnel were very efficient. It only took 30 minutes to go through: a very thorough security line where people got asked questions, then a check-in baggage security check, then the airline counter check-in, then a carry-on baggage security check, then passport control. Not once did we take our shoes off or take out liquids! Israel is all about profiling - something they don't apologize for because it works, and makes our TSA look like the amateurs.
Just remember to check your terminal, Terminal 1 or 3. Most international flights seem to fly out of Terminal 3, but not a guarantee.
USING PUBLIC TRANSPORTATION TO THE OLD CITY AND MOUNT OF OLIVES
As far as the map goes, it looked like an easy 30 minute walk to the Old City. What the map didn't mention is how hot the sun is and the numerous hills to climb! Plus, getting to the gate of the Old City is one thing, but there's a lot more walking to do within the walls! The best starting point for the Via Dolorosa (Way of the Cross) was the Lion's Gate in the Muslim quarter. The entrance for both the Dome of the Rock and Western Wall is near Dung Gate. You can explore the sites around Mount Zion outside of Zion Gate in the Armenian Quarter. All this is in a "compact" area, but somehow stretched into long days of exploration. If walking is difficult, we actually saw bus number 38 within the wall confines, stopping at the major gates.
Unfortunately, the tram only runs in a westerly direction from Damascus Gate along Yafo Street and back. It was useful in getting to Mount Herzl to visit the Yav Vashem Holocaust Museum, but the tram didn't go anywhere near our neighborhood to the south. In our 'hood, there were plenty of green West Jerusalem buses (Egged) that ran along Emek Rafaim Street, and after some trial and error, we stuck with bus number 18 that took us all the way to the front of David Citadel Hotel on David Hamelech Street. From this stop, the Jaffa Gate (Old City) and Yafo Street (City Center) was only a 5 minute walk. We couldn't find an reliable transit map because apparently, the bus schedule changes 'all the time.'
The central bus station for the white (with blue writing) Arab buses is in front of Damascus Gate. These buses service East Jerusalem, and we took bus number 75 to get up to the top of Mount of Olives. Suddenly, we were surrounded by passengers with veils and scarves over their heads. We couldn't believe the stark segregation in just a matter of 1 or 2 city blocks. Once the bus got going, there were no formal stops. People just told the driver where to stop. We got off at the highest point on Mount of Olives, close to the Russian Church of Ascension and walked towards the Mount of Olives Hotel where there was a nice lookout point.
From the top of Mount of Olives, it was a very steep but easier hike going down than trying to hike up. We stopped by the Garden of Gethsemane at the foot of the mountain, then made our way back to the Old City.
We didn't attempt any out-of-Jerusalem visits to places Bethlehem, Nazareth, Galilee, Dead Sea, etc. so we are unable to provide any information on public transportation to these areas.
VISITING THE SITES
If you have a smart phone, we recommend downloading the "Jerusalem Old City Audio Walking Tours" a self-guided tour; unless you're into joining one of those organized tours. There are literally hundreds of churches, synagogues, or mosques built upon significant sites. So, to see anything, you're going to be stepping into a lot of places of worship. They do not charge an admission fee, but require that visitors respect their hours and dress code. Just leave the shorts and tank tops at home and bring pants, longer skirts, shirts with sleeves, and a scarf. Also, the most popular sites get very crowded so plan to start the day early. We thought we were proactive by showing up at the Dome of the Rock line at 7:30 am for an 8 am opening and the line was already over an hour long.
HOLIDAYS AND THE SABBATH
Remember that the Jewish sabbath is observed from Friday sunset to Saturday sunset. This means that most businesses and transportation close well before sunset in preparation for the sabbath. We were lucky to have a kitchen in our apartment where we stocked up on groceries and stayed in. Little did we know that we would be repeating this again for the Sukkot holidays when everything shut down again on a Sunday through Monday. The hotels probably operated as usual, but a good tip is to look up any Jewish holidays in advance so you can be prepared for limited hours and closings.
SAFETY
We were anxious about some of the world events leading up to our arrival in Jerusalem (American embassy raids, Islamic protests, Iran nuclear weapons, etc.), but we knew Israel is very serious about its security so we felt quite safe, once we arrived. We saw a lot of security around transport hubs and onboard the trams, which made us realize it's been years since we heard of any suicide bombers blowing up buses and trams in Israel.
We made the mistake of hanging around Lion's Gate in the Muslim Quarter on a Friday right before their prayer was to begin as literally hundreds of Muslim poured in through the gate to the Al-aqsa mosque. Any kind of Islamic protest seems to occur after their weekly Friday prayers and sure enough, we saw plenty of Israeli military and police with their riot gears. Although it was peaceful on that particular day, we could've easily been caught up in this mess a week later, "Friday Prayers End in Riot on Temple Mount". There's also some word of caution through Jerusalem/Old City Wikitravel about visiting the Temple Mount and Muslim Quarter, that seemed quite accurate.
Overall, we're glad we stayed in a residential neighborhood and didn't pack our agenda with too much stuff. Not only did we thoroughly enjoy this once-in-a-lifetime opportunity to visit the holy sites, but the Jewish cultural immersion was a good experience, while the ambience of the holidays gave us another unique perspective of their heritage.
Shalom!