Intranet is very important.
If you want these documents to be available to the general public, then the tools you can use are more or less restricted. Any modern word processor worth its salt can do automatic generation of table of contents, pagination, layout of headings and sections, and have excellent print quality. Thus your document should be available in print-out format if you want these. Now this means you want an HTML version out. So what you do is create the document in a word processor so you can edit it easily in all the ways you mentioned, convert it to HTML using a good converter so people can easily browse it online, and offer the original document as an alternative for people who want to print it with high quality.