Quick background: i'm the portal admin for our medium sized company. Currently, our intranet policy is to try to integrate everything into our intranet portal, (which we use mostly as a CMS, with a handful of applications integrated as well). This means that all of our software appears to the end user to come from one site, which is good. But it also means that we have to modify just about every piece of software that we want to incorporate into the website to fit into the portal. The disadvantage of this is that each component of our portal (the cms, the blogging, forums, etc) are not best-of-breed, and to be quite honest, they are pretty bad compared to their free and open source counterparts (wordpress, phpbb, mediawiki, are examples that come to mind). Because the users are forced to use these subpar tools, they aren't happy.
We are currently looking at the other end of the spectrum, where each piece of software in our intranet isn't integrated, but we are able to use best-of-breed free software. We would be able to much more rapidly roll out new services to our company, but the down side is that the services wouldn't be integrated. A users profile in wordpress (movable type, in our case) is not connected to their profile in the other applications, for example. The software overlaps, finding information is more difficult, users aren't happy either.
How does your company balance the ability to rapidly integrate new tools with the desire to have a single coherent interface presented to the user? Do you pick one enterprise platform and force yourselves to stay wtihin its boundries or do you attempt to provide cohesion between many disparate tools?