I've used TWiki in the past. I like it. It's very powerful but still based on simple concepts. It features:
- "normal" wiki behaviour: formatted editing (today it's wysiwyg I think), auto-links, tables, attachments etc.
- complete revision control.
- generated text, eg. TOC. There is also a kind of "query". You can make a query to the topics and show title, summary and special 8also user defined fields) in columns. This is very powerful, you don't need to maintain these tables manually.
- for documentation you can also put topics together by using includes or queries.
- You can defined predefined texts for reuse ("Twiki Variables");
- Structured data: in a topic you can define a data structure and assign this as a Twiki Form to any topic. When editing it, it is shown as check boxes, drop downs, text fields etc.
- Mail notifications
- Access rights
- lots of plugins, for instance a powerful spread sheet plugin (with formula resolver etc) and lots of others for almost anything you can think of.
Using these features and some basic html (in topics of course) you can actually write simple web applications.
It stores everything into text files, so you don't need to maintain a database.
There is much more, I forgot about it. These are just the things I miss in other comparable tools. At the end, you need much of this stuff...
Integration into other tools is usually very simple, you can use hyper links to point from one web application to the other, that's usually enough. There are also plugins for some issue tracking systems.
The downside is, it is so powerful that you will spend some time to create your "applications" (but then it scales and can easily be adapted to new requirements). Another problem was to install it on a windows machine without using Cygwin. They simplified this a lot in the last few years. (See the installation guide, "TWiki is straightforward to set-up on Windows"...)
If you think you need something sophisticated, it's worth to try!