We just finished one project with IBM Portal 6.1 and IBM WCM 6.1. Honestly I wasn't too happy how those two products were integrated. Biggest problems were that WCM navigation and portal navigation are totally different things and it creates problems with bread crumbs and sitemap, secondly IBM WCM API is so slow that we needed to write couple of hacks to get it working with normal speed. I have been looking around for a while and haven't found any WCM + Portal integration that I truly like. Common problem seems to be that WCM systems are built to work alone without portal server and thus there are overlapping functionalities which are not handled properly when integrating those two things.
I give it some thought and tried to come up with some solution how this integration can be done. Basically idea is to let WCM deal with content versioning, syndication, security, etc but when it comes to navigation and presentation then that part should be covered by portal side. I created one google doc explain the idea - https://docs.google.com/document/edit?id=1PT5RYuJqhUotXmoMZOBw88uFlKiDOIGYCoBQOEkfOUc&hl=en&authkey=COjQzJ8D. Would be grateful to get your ideas.