A thread on the Temples, Religious Monuments and Centres of learning that were destroyed or desecrated in what is now present day India, Afghanistan and Pakistan: 
The Golden Temple (Harmandir Sahib) located in Amritsar, Punjab, India, was attacked multiple times by the Mughals as well as the Afghans under Ahmad Shah Durrani, who desecrated and destroyed the Temple in 1757 and again in 1762. It was later rebuilt properly by Ranjit Singh ji.
The desecrated Martand Sun Temple located in the Anantnag, Jammu and Kashmir, India, was fully built during the 8th Century and is dedicated to Surya Dev (the solar deity in Hinduism). It was desecrated/partially destroyed by Sikandar Shah Miri in the early 15th century CE.
Nalanda, an ancient centre of learning, located in Nalanda District, Bihar, India, was fully completed during the 5th century under the reign of Kumaragupta I. It was partially destroyed and ransacked between the late 12th century and early 13th century CE by Bakhtiyar Khalji.
The Buddhas of Bamyan, Afghanistan were two 6th century CE statues of Gautama Buddha that went through a series of attacks by Invaders such as Aurangzeb and Nader Shah until they were finally destroyed by the Taliban in 2001.
Somnath Temple, located in Veraval, Gujarat is a temple that was desecrated, destroyed and looted multiple times by various invaders including Mahmud of Ghazni in 1024 and Alauddin Khalji in 1299. It was later fully rebuilt in 1951.
Gyanvapi Mosque was originally the site of the current Vishwanath (Shiva) Temple located in Varanasi, Uttar Pradesh, India. The Temple mentioned in the Skanda Purana, was destroyed multiple times by various Invaders, with the most recent one being Aurangzeb in 1669 CE.
Babri Masjid (now demolished), located in Ayodhya, Uttar Pradesh, India, was a Mosque that was built upon the original destroyed Ram Janmabhoomi Temple (birthplace of Lord Ram) by Mughal Ruler, Babur.
Sharda Peeth is a ruined Temple and ancient centre of learning located in Neelam Valley, POK. It is said to have existed for thousands of years, but more conservative estimates state that it was likely built under the Kushan Empire, Lalitaditya, or by various rulers in stages.
The Shahi Idgah Mosque, located in Mathura, Uttar Pradesh, India that stands adjacent to the present Krishna Janmabhoomi Complex (birthplace of Lord Krishna) was built upon the original Keshavdeva Temple that was destroyed by Aurangzeb.
There are possibly thousands more Temples, Religious Monuments and centres of learning that have been destroyed over centuries but these are the more notable ones.
