I'd like to write some documentation that will be written in sections (1.1, 1.2, 2.1, 2.2, 2.3, etc). I'd like to use something that will generate the table of contents in the end or at least have it "linked" up so that when I make changes everything is still accurate (if I merge section 2.1 and 2.2 or something).

The end result needs to be in pdf. I don't want to pay $350 for Acrobat Pro either...

I've got microsoft word, but every little thing is a pain (for example, having one background of a page be a different color than another).

Any ideas on how to create quality documentation in a pdf format?