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At Base22 we use Confluence as our documentation wiki
We used to use a custom theme which we developed called PopKong which server us well but got to be a hassle to update everything Atlassian rolled out a new version so we just switched to the Out of the box theme and let popkong go open source.
The Documentation theme that comes with Confluence actually has a lot of the same features that old theme used to have and is surprisingly easy to customize.
Step 1 Apply the theme
- As Space Admin go to Browse > Space
- Select the Documentation Theme
- After it is applied you will notice a new option to configure the theme
Configure Theme 
- In the configuration section you will see a place to add wiki markup to the header, navigation, and footer
- I added a simple footer with copyright information
- Put the logo in the navigation section and made it a link to the home page of the space. To get the path I just right clicked on the existing logo that was already uploaded. Even when it is turned off (see below) the path still works. Any thing you put in the navigation section will appear above the pagetree on the left.
Change the stylesheet
I then went into the stylesheet and changed the header to grey with with an orange border to match the logo and the overal look I wanted.
Move the logo
Since the logo is now in the navigation area, I clicked No to hide it from the space.
Thant's it. I may make some additional changes like adding discus comments, a supper footer, and reintroduce the site navigation into the header from base22.com but those require some more prep. This was all done with the out of the box tools the theme provides.