The major systems of transliteration used by Slavic scholars in the United States are the Library of Congress system (most often used without the additional diacritics), and what J. Thomas Shaw calls the International Scholarly system, which is closest to the ISO R9 & Slavic Review systems, but which in place of "kh" or "h" uses "x" for Cyrillic "x." The paternity of this system is rather suspect, but it has been used widely since referenced in J. Thomas Shaw's 1967 reference work The Transliteration of Modern Russian for English-Language Publications. Madison: University of Wisconsin Press.
There are a number of factors that may dictate the use of a particular system over another. Shaw elaborates on his own method for selecting a system based on usage & intended audience. While this approach to selecting a system is sound, Shaw's method confuses the issue by allowing for the use of several systems within a single document.
Most scholarly publications indicate their preferred system of transliteration with their information for prospective contributors. In very general terms, linguistic-oriented publications tend toward the International Scholarly system (or some other system based on Croatian), while literature/culture publications tend toward the LC system w/o diacritics.
Students and scholars in Slavic studies should be able to recognize, read, and transcribe using both the LC system without diacritics and the International Scholarly system (or other similar system). They should also have a general knowledge about the range of possibilities for the transcription/transliteration of Cyrillic using other systems.
For examples of these systems in practice, go to the Transliteration Practice page. For tools and strategies for searching for transcribed or transliterated forms of words on the Internet or in library databases, go to Transliteration Primer & "Cheat Sheet" for Database/Web Search Strategies.