Currently the customization of the left menu is only possible by modifying the JSP file that builds the menu. We plan to add a link manager (actually, we plan to add a full wiki....)

To add items to the tree, edit the file /desknow/jsp/original/MenuBody.jsp with a text editor and add lines like this towards the bottom, just before the ];
,['Link 1','http://www.desknow.com',tf,admin_group]
,['Link 2','http://www.google.com',tf,admin_group]

admin_group defines the icon to use, and is defined in /desknow/3.1.11themes/templates/TreeFormat.jsp 

(obviously replace 3.1.11 with your current version number!)

use '_blank' (with the quotes) instead of tf to open in a new window:
,['Link 2','http://www.google.com','_blank',admin_group]

If you want to include the username in the URL:

,['Link 1','http://my.site.com?username=<%= account_username %>&domainname=<%= account_domainname %>',tf,admin_group]

Important: make a backup copy of the MenuBody.jsp file before modifying it. When you upgrade DeskNow, you must upgrade the file as well.