Menu links not working in Ubuntu (D7)
My suspicion is that Drupal's .htaccess URL rewrite directives have been disallowed in your Ubuntu installation of Apache. If it were a bootstrap or database connection problem, you would not be able to see the front page either.

Ordinarily, Drupal prevents Clean URLs from being activated if not supported by the server. In this scenario, of course, that test was done in the Windows installation. Ensuring rewriting support in the target server is at the top of the migration checklist.

The quickest way to see if Clean URLs is the culprit is to try browsing to localhost/sitename/index.php?q=user/login ; if that page does come up, you will need to enable rewriting in your web server.

See http://drupal.org/node/1186762#comment-5424052 for some instructions on checking your Apache configuration to make sure it allows Drupal to rewrite URLs in its .htaccess file.

If you can confirm that the .htaccess file is being read, rewrite directives have been allowed in Drupal's installation directory, and that mod_rewrite is active, and still see problems, I would check next for a corrupted menu table.