What is APexDoc in Salesforce?

ApexDoc is a java app that you can use to document your Salesforce Apex classes. You tell ApexDoc where your class files are, and it will generate a set of static HTML pages that fully document each class, including its properties and methods.

We use just standard JavaDoc to document our code. It's a pretty nice standard and it allows you to run SfApexDoc against your code to have a more easily browsable code base. You might also want to look at this post to see how you can see what code/methods are not being used (full disclosure: I've not had a chance to try this out, but I know Andy and it should at least be worth looking at).
As for documentation of workflows and other things, we make an effort to have every one of our fields documented in our objects (even if it's putting a description of [UNUSED] in them). We've written some internal tooling that displays object data on an angular page so that our external developers know the API names and structure of the objects.
The biggest thing that has helped us as for as an organization goes is storing everything in git and having each commit tied to a unit of work either a User Story (from rally) or a Bug (from Bugzilla). This way we can look back at history to see what has been done and who did it. It was a little tough to get our non-developers over to git but it was worth it in the long run.