By default the links on the left navigation ( Quick Launch) in Enterprise Portal opens up in the same window replacing the current page.If there is a need to open up specific pages in a new window , )for example you are viewing the sales order list page and the Sales Report link on the left navigation should not replace but open up in new window ), then you can achieve this by changing the url property of the web menu item.

For example , if the URL for EPSalesStatistic ( Sales – All Reports) by default points to Enterprise Portal /EPSalesStatistic.aspx.
Change this to 

and Refresh AOD to clear the metadata cache on the portal.

From then wherever this link is used, now the page will open in a new window.