Your pages are missing the required YAML front-matter (http://jekyllrb.com/docs/frontmatter/).
For example, your wiki.html page, at the very least, will need
---
title: Wiki
---
<!-- Begin already existing code here... -->
<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
Once the YAML front-matter is added, you should see them show up anywhere you call site.pages