Are there any good documentation templates for SharePoint sites available? I have created a few SharePoint team sites and I would like to document all list, doc libraries, permissions...etc
A Wiki Page Library is a type of Document Library that contains Wiki Pages. Wiki Pages are very easy to edit - you can simply paste content directly from Word if you want, and all formatting, including images, tables, etc., will be kept. Wiki Pages also have a nifty syntax for linking to other pages which can be used to link supplemental info or create a table of contents.
In my experience Wiki Libraries are far superior to Word docs sitting in document libraries because users are much more inclined to actually read them.
Wiki Page Libraries are really well suited to documentation, and the web is full of wiki-formatted documentation for software projects, though not necessarily SharePoint wikis. Off the top of my head I can think of MineCraft, Blender, Open Office, and Python.