Pekka,
I looked in to this previously, I think you can use pdftk (a command line utility), to fill in a PDF form using FDF/XFDF data files, which you could easily generate from within PHP. That was the best option I've seen so far, though there may well be a native library.
pdftk is quite useful in general, worth having a look at.
Update: Have a look here: http://php.net/manual/en/book.fdf.php
