Fodor's - highest rated on Amazon; their book is the most up-to-date
Lonely Planet - book gets poor reviews on Amazon (political, not enough practical advice...but may be best for those planning on significant time in the Palestinian Territories)
...various other "pilgrim" and "spiritual" guides to the holy sites
Ali Karavan / Abu Hassan Hummus - 1 HaDolphin (Dolphin St.), famous for mesabaha and "the best hummus in Israel", Hungry in Tel Aviv, Food & Wine, this blog discusses how to get there, open ~7:45 am - ~2:45 pm (not on Saturday??)
Abulafia Bakery - 7 Yefet St, Food & Wine
Dr. Shakshuka - 3 Beit Eshel, 03-6822842, S-Th 8-mid, Fri 8-Shabat, Sat 7 pm-mid, Libyan food, known for the eponymous shakshuka and other middle eastern favorites (couscous, kebab, etc.), rec'd by Frommer's, Food & Wine, Fodor's (book, but curiously not online)
Abu Marwan - hummus place rec'd by Hungry in Tel Aviv
Church of the Holy Sepulchre - allegedly the place where Jesus was crucified and buried. See church website for worship times and hours, and also very good information from Sacred Destinations andWikipedia. The church is shared by 6 different Christian denominations under the awkward "Status Quo Agreement", which thus occasionally causes brawls as the sects compete for dominance. The oddest such dispute is over the "immovable ladder", so called because the Armenians control the window but the Greeks control the ledge on which it rests...and thus it has remained since the 19th century.
Old Town & Nearby
Lina - Christian Quarter 42, 02-627-7230, like In-n-Out they have a limited menu but they do it well...they only have hummus and masabaha. Both are excellent; I especially liked the hummus (by far the most flavorful I had in Israel--perhaps they add more garlic?).
Abu Shukri - 63 al-Wad, 02-627-1538, one of the best hummus places in Jerusalem; a nice place for lunch, since hummus also comes with falafel and other sides; unlike the purists at Lina, they also do kebabs, etc.
Eucalyptus - great restaurant just outside the Jaffa gate (turn left and head down the street a block or so), lots of interesting flavors. Don't miss the chicken-stuffed figs!
Central (West) Jerusalem