Here are a listing of popular shuls and communities:

DoDaven always has useful general info.

Rabbi Wein’s Shul on Rechov Ussishkin, in Rechavia – ‘‘Beit Knesset Hanassi”

Katamon Shteiblech – More like a minyan factory. First Shacharit at 5.55. Every 15 minutes until 9ish. Last Maariv at 12pm.
Ramban: A real community. Good shiurim in Ivrit and English.
Shir Chadash: A popular community for English speakers run by Rabbi Ian and Rachel Pear.
Yakar: Very popular for Israel and Anglos. Melodious davening and interesting shiurim in Ivrit, English and Russian.
ELC: Growing English speaking community and Kollel in Emek Refaim.
Eretz Chemdah – 2 Rechov Bruriya. Shabbat Minyan, with pre-shacharit shiur and Drasha and kiddush each week.
Nitzanim: Well run and friendly community in Baka. Popular with native Israelis and Olim.
Mayanot: Mayanot is a popular community in Nachlaot. Especially nice davening on Friday night.
Great Synagogue: Especially popular over the Chagim. Often has guest Chazanim and speakers.
Yedidya: Well run community in Baka.
Chabad Baka:  104 Derech Bet Lechem.
Chabad Rechavia: Top of Rechov Ramban.
Kol Rina: 26 Rechov Beersheva, Nachlaot.
Simchat Shlomo:  18 Hagilboa, Nachlaot.
Ohel Nechama:  3 Chopin, Katamon.

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