I'm not a Perl user but I imagine you'll struggle to find a better free text extractor than pdftotext.
pdftotext usually recognises non-ASCII characters fine, is it possible it's extracting them ok but the app you're using to view the text file isn't using the correct encoding? If pdftoetxt on windows is the same as the one on my linux system, then it defaults to exporting as utf-8.
Take a look at PDFBox. It is a library but i think that it also comes with some tool to do text extracting.
You may never get an appropriate solution to your problem. The PDF format can encode text either as ASCII values with a font applied, or it can encode it as a bitmap. If the tool that created your PDF decided to encode the special characters as a bitmap, you will be out of luck (unless you want to get into OCR solutions, of course).
These modules you can acheive the extract text from pdf
From CPAN
my $pdf = CAM::PDF->new($filename);
my $pageone_tree = $pdf->getPageContentTree(1);
print CAM::PDF::PageText->render($pageone_tree);
This module attempts to extract sequential text from a PDF page. This is not a robust process, as PDF text is graphically laid out in arbitrary order. This module uses a few heuristics to try to guess what text goes next to what other text, but may be fooled easily by, say, subscripts, non-horizontal text, changes in font, form fields etc.
All those disclaimers aside, it is useful for a quick dump of text from a simple PDF file.