Barfield, Thomas.  “Turk, Persian and Arab: Changing Relationships between Tribes and State in Iran and Along its Frontier,” in Nikki Keddie and Rudi Mathee, eds. Iran and the Surrounding World (Seattle: University of Washington Press, 2002), pp. 61–86.

Bregel, Yuri. An Historical Atlas of Central Asia.  Leiden: Brill, 2003. It’s expensive, but there’s no better collection of maps and historical text.

Burton, Audrey. The Bukharans: a dynastic, diplomatic, and commercial history, 1550–1702.  St. Martin’s Press, 1997.

Geiss, Paul Georg. Pre-Tsarist and Tsarist Central Asia: Communal Commitment and political order in change, London: Routledge, 2003. Provides concise political histories of Central Asian tribes and kingdoms. Use in short excerpts or for advanced students; the writing is dense and sometimes the English is convoluted.

Levi, Scott and Ron Sela, eds.  Islamic Central Asia: An Anthology of Historical Sources.  Bloomington, IN: Indiana University Press, 2010.  A terrific collection of primary sources.

Levi, Scott. The Indian Diaspora in Central Asia and its Trade, 1550–1900. Leiden: Brill, 2002.  Readable, deeply-researched and very unusual approach to Central Asian history. Levi studies the Hindu traders who built networks connecting Central Asia, Mughal India and Iran.

Millward, James A. Eurasian Crossroads: A History of Xinjiang. New York: Colombia University Press, 2007. The only survey of Xinjiang history, based on extensive knowledge of primary sources. Can be very dense reading for students.

Millward, James A. Beyond the Pass: Economy, Ethnicity, and Empire in Qing Central Asia, 1759–1864. Stanford, CA: Stanford University press, 1998.  A detailed account of trade patterns between Chinese and Central Asians, written in a lively and accessible style. Covers trade, taxation, and the people involved in this Asian “wild west.”
     
Perdue, Peter C. China Marches West: the Qing Conquest of Central Eurasia. Cambridge, MA: Belknap Press of Harvard University Press, 2005, Chpt. 3, “Central Eurasian Interactions and the Rise of the Manchus” has a terrific and clear discussion, with maps, of the Zunghars/Oirats.

Soudavar, Abolala. “The Early Safavids and Their Cultural Interactions with Surrounding States,” in Nikki Keddie and Rudi Mathee, eds., Iran and the Surrounding World (Seattle: University of Washington Press, 2002), pp. 89–120.  Excellent short study of rivalries and interactions among Safavids, Uzbeks and Ottomans in the 16th century.