Bukhara was an early outpost of Islam, and the religion radiated from there throughout Central Asia. The mystic Sufi branch was particularly important here, with the Naqshbandi sect holding sway thoughout much of the area.
Bukhara had over 100 madrassas and 300 mosques. From the beginning, Islam placed great value in learning, and madrassas (religious schools) are among the most important buildings. The word has recently become associated with fundamentalist indoctrination academies, but most madrassas are just Islamic colleges. Some of the impressive buildings in Bukhara date back to the 15th century. 
Although there has been a small religious revival since independence, most of these structures are still unused or converted to souvenir shops. Many smaller madrassas have been renovated into B&Bs with comfortable bedrooms and modern conveniences. We stayed at one with eight rooms and an 18th-century mosque in the back. 
Even the more obscure buildings have beautiful features, like this wooden ceiling in a small neighborhood mosque.
The tallest structure in Bukhara is the Kalon (great) Minaret. Built in 1127, it is 47 meters (160 feet) tall with foundations another 10 meters (33 feet) deep. With only minor repais, it has survived earthquakes and Bolshevik air bombings. Even Ghengis Khan left it alone. In addition to its religious uses, the Emir found it a convenient place for executions, dropping prisoners to their death. Bukhara was also a temporal power superior to Samarkand for most of its history. For the last few centuries before the Russians moved in, Bukhara was the seat of a notorious emir, who capriciously tortured and killed prisoners including two British agents who blundered in. His fortress, the Ark, was a place best avoided.
I gathered my courage and climbed the "water tower," a decaying Soviet structure in the Registan square opposite the Ark. It seemed solid enough, but I refrained from trying the last external staircase to the top floor. Marcia stayed on the ground and refused to look. The oldest surviving building is the mausoleum of Ismail Samani, built in 905. The building's decoration includes suns and other Zoroastrian motifs. By the time of the Mongol invasions, it was covered by dirt and invisible.
Bukhara is known for its medieval markets, built as a series of stone domes. These are now given over to souvenir shops, but still fun to walk through. 
Lacking an association with the government's favorite strongman Timur, Bukhara has seen less reconstruction funds and wholesale rebuilding. As a result, it has a more authentic feeling with occasional locals still using the historic structures. In one neighborhood, a man invited us into his "private museum," a 19th-century madrassa fallen into disrepair.
We also visited the 19th-century mansion of the first Communist president of the Uzbek SSR. He was hardly a member of the proletariat.
A few kilometers outside Bukhara lies the Bakhautdin Naqshband Mausoleum, the burial place of the founder of the local line of Sufi mystics. Pilgrims come from afar to visit his tomb and to walk around the trunk of an old tree, which supposedly sprouted at a place where Bakhautdin struck his staff on returning from Mecca. This practice is more likely to have come from the local Zoroastrian tradition than from Islam.
