In the past week or so, JSWolf and I have been troubleshooting a problem with certain characters not displaying properly in FBReader (see http://www.mobileread.com/forums/showthread.php?t=14703
). I also sent samples to Nikolay Pultsin (the author of FBReader).
After a few email exchanges, Nikolay informed me that today, he released a new version of FBReader. Along with some other bug fixes, this new release adds an "Encoding" option to the program options, where you can set a "default" encoding for all newly opened ebooks. Note that if you have previously opened an ebook in FBReader, the character encoding is remembered, so you will have to individually set the encoding for that ebook under the "Book Info". I think you only have to do this for the last ten ebooks that you have opened in FBReader.
In the example that JSWolf and I were having trouble with, setting the encoding to "Western (windows-1252)" fixes the display problem for me. This should be good for anyone in the US or Western Europe, unless you have setup Windows for a language that uses a different code-page.