Many of my customers has asked for a simple way to add existing web based applications to Alfresco, so that Alfresco is their main gateway to all applications. I have done this for them by customizing the Share Header to add menu links, and then by using an iframe. By using an iframe, you still have access to all Alfresco menus for easy navigation. Not all applications are iframe friendly, so those you can add as links that open in a separate window. And yes, putting application in an iframe is not true integration and does note make Alfresco a true portal, but for almost no cost at all it does add value.
