I have written a small proof of concept that parses the file czech.pdf. This file contains several characters with diacritics. It was created in answer to the following question: Can't get Czech characters while generating a PDF
The text is stored in the file twice: once using a simple font, once using a composite font. In my proof of concept (named ParseCzech), I parse this PDF to a file encoded using UTF-8 (UNICODE):
public void parse(String filename) throws IOException {
PdfReader reader = new PdfReader(filename);
FileOutputStream fos = new FileOutputStream(DEST);
for (int page = 1; page <= 1; page++) {
fos.write(PdfTextExtractor.getTextFromPage(reader, page).getBytes("UTF-8"));
}
fos.flush();
fos.close();
}
The result is the file czech.txt:

As you can see from the screen shot, the text is extracted correctly (but make sure that the viewer you use knows that the file is encoded as UTF-8, otherwise you may see strange characters instead of the actual text).
Note that some PDFs do not allow text to be extracted correctly. This is explained in the following video: http://www.youtube.com/watch?v=wxGEEv7ibHE
Please share your PDF so that people on StackOverflow can check whether you don't succeed to extract text because of an error in your code, or whether you don't succeed because the PDF doesn't allow you to extract the text.