Shuls

Chabad

Ramat Aleph, 10 Dolev, Heichel Menachem

Ramat Aleph, 4 Tzelim, near corner of Kishon, Ohr Tzvi and Menucha

Ramat Aleph, Shchunat Mishkafayim, HaRav Kook Street 22

Ramat Aleph, Sorek, in Shaaleh Torah school, Ohr Lubavitch

Shchunat Cheftziba, Ben Ish Chai Street 5

Yofe Nof, Rechov Ben Asai 18

Ramat Avraham, Mayanei Yisroel, 2 Rav Yisroel Grossman

Ramat Beis, Chabad of Beit Shemesh, Hanasi 1 (There's a Mayanei Yisroel group here)

Ramat Beis, Sderot Rabi Me''ir Ba''al HaNes 8

Ramat Beis, Chabad Zanuahk, Rival 43

Ramat Gimmel, Havakuk HaNavi St, 7  https://chabadg.co.il/en/homepageen/

Ramat Daled, Rav Zeira 6, Dira 5

Ramah Daled, Mar Ukvah 8

Kirya, Mayanei Yisroel 13 Ohr Somayach St.

בבית הכנסת חב''ד יפה נוף, בן עזאי 18.

Old Beit Shemesh, Rechov Rabin 11

Old Beit Shemesh, Rechov Rakeft 8, בית מנחם גבעת שרת

Mayanei Yisroel is a movement of Chabad chassidus that is culturally similar to Yerushalmim and other Chassidic groups. This means long coats, long payus, no smartphones, strong anti-Zionism etc. Many of the participants are Yidden who group up in those groups, became attracted to Chabad Chassidus, but maintain their mode of dress and other features of those groups. 

Yeshivas

Ramat Gimmel, Yeshiva Gadolah, Achiya Hashiloni off of Nehira HaNovi

Ramat Gimmel, Yeshiva Gadolah in English, at the shul on Habakuk St.

Ramat Beis, Tiferes Shmuel, Cheder, Rebbe Meyer Baal Haneis

There's also a yeshiva ketana and several ganim.