http://www.mockflow.com/ has a free version, you will need to register to use the free version and be able to download and use their desktop version, i recently have registered there and did exactly that, ive yet to use it so cant comment on whether i like it or not, it allows for Multi page PDF document. Theres also something about Generate Specification in MS Word format, but i haven't read that yet.
If you search both on here though and at http://stackoverflow.com/ there really are lots of tools for this, some allow for certain things that others dont, some more interactive than others.
Once ive got something on paper i will probably stick with mockflow as im no designer or developer and only need to be able to take my paper skectches eventually from that to online.