1) The Illustrated Guide to The Protozoa, second edition, Volume I and II, Edited by J. J. Lee, G. F. Leedale, P. Bradbury, Society of Protozoologists, Lawrence, Kansas, 2000     It is a professional, comprehensive, very well illustrated guide to the protozoa. Includes useful protozoa drawings and excellent SEM images. Also, discusses contemporary taxonomy of the protozoa.
2) How to know the protozoa, Theodore L. Jahn, Eugene C. Bovee, Frances F. Jahn, second edition, The Pictured Key Nature Series, Wm. C. Brown Company Publishers, Dubuque, Iowa, 1979     Very nice book - a key to identify the most common species of protozoa.
3) Free-Living Freshwater Protozoa: A Color Guide, D. J. Patterson, John Wiley & Sons, 1996     A wonderful guide to the protozoa.
4) A Guide to the Protozoa of Marine Aquaculture Ponds , D. J. Patterson, M. A. Burford, CSIRO Publishing, 2001     A nice guide the marine protozoa, describing their biology and characteristics. Over 50 richly illustrated pages, including color images.
5) Protozoology, R. R. Kudo, fifth edition, C. C. Thomas Publisher, Springfield, Illinois, 1966     A classic textbook of protozoology. It is an excellent guide, very well illustrated. Over 1100 pages and almost 400 figures.
6) General Protozoology, V. A. Dogiel, revised by J. I. Poljanskij and E. M. Chejsin, second edition, Oxford University Press, 1965     Another classic textbook of protozoology. Although a little bit outdated, it contains many useful information and numerous pictures and figures. I found the 'Ecology of Protozoa' chapter particularly interesting. Many references.
7) Introduction to Protozoology, Reginald D. Manwell, second revised edition, Dover Publications Inc., New York, 1968
8) The Biology of Protozoa, Michael Sleigh, Edward Arnold, London, 1981
9) The Biology of Paramecium, Ralph Wichterman, The Blakiston Company, New York, 1953    A classic book on biology of one of the most common protozoans - Paramecium.
10) Blepharisma. The Biology of a Light-Sensitive Protozoan, Arthur C. Giese, Stanford University Press, Stanford, 1973
11) Seashore Life Between The Tides, William Crowder, Dover Publications Inc., New York, 1975 (reprint of the 1931 edition)     Describes marine life of the Atlantic shore. Covers several genera of marine protozoa. Great illustrations by the author.
12) Wimpertiere oder Ciliata, A. Kahl, Hamburg 1935     Amazing, very detailed guide to Ciliates.     In German. Available online from Digital Image Books
13) Das Protistenreich, Ernst Haeckel, Leipzig 1878     In German. You can access this book here. Comes from the Kurt Stüber's Online Library
14) Die Radiolarien, Ernst Haeckel, Berlin 1862     Amazing drawings of the Radiolaria specimens.     In German. You can access this book here. Comes from the Kurt Stüber's Online Library
15) Report on the Radiolaria collected by H.M.S. Challenger, from Report on the SCIENTIFIC RESULTS of the Voyage of H.M.S. Challenger during the years 1873-1876, Ernst Haeckel, London 1887     Even more detailed and amazing guide to Radiolaria, over 1800 pages and hundreds of very detailed illustrations (140 color plates).     You can access this book here. Scanned by David C. Bossard, available from the Kurt Stüber's Online Library
16) A Field Guide to Bacteria, Betsey Dexter Dyer, Cornell University Press, 2003     A fascinating book describing free-living species of bacteria.
17) Exploring with the microscope. A book of discovery and learning., Werner Nachtigall, Sterling Publishing Co., Inc., New York, 1996    Amazing book on microscopy and photomicrography of various subjects. Includes very extensive introduction to microscopy and covers many advanced topics. Includes keys for identification of aquatic microorganisms. Illustrated with hundreds of beautiful photographs. Beware! You WILL get addicted to microscopy after reading this book!