I make hundreds of manuals in pdf form mainly using Adobe 8. But another good program is Lyx. This program is free and can create marvelous documents in many forms including pdf. It takes a bit of learning but it is amazing what it can do with index and references etc all automatically generated
http://barry.sarcasmogerdes.com/stel..._guide-new.pdf
Another program that was recomended to me was Nitro. This is a very versatile pdf generator but not free (quite cheap ). However I paid for it and installed it on my old XP but when I wanted to transfer it to my main computer I found it is a single licence and would need to pay for every computer. I have not used it again because the computer it is on is broken.
Here is a document with embedded hyperlinks to a range of pdf's I have made.