Too often, people like to install anything and everything into SharePoint, with a goal of SharePoint being their single corporate portal. Unfortunately, when a product is updated, the amount of time required for testing is daunting and expensive.
Most people will say the single solution to this is well defined governance; defined rules and policies regarding the organization’s use of SharePoint. This approach can work. Such a policy might say that the organization will have exactly one SharePoint site, and anything which attaches to it includes lifecycle management, costing the owner $$$.
Realistically, while it is good to have such a policy, it is equally important to simply define the line in which one system ends and another begins. Generally speaking, this tends to be defined by Service Level Agreements (SLA). For example, a dashboard using Reporting Services with the source data in SharePoint would likely make sense to integrate tightly, while TFS may use its own SQL servers and should therefore remain independent (other than perhaps a link or IFRAME).
One of the really cool features of SharePoint 2010 is the ability to share services across SharePoint installations. So if I want to provide personal sites to everyone in the company, and I have four departments--each of who want their own installation of SharePoint--I can still keep all of the personal sites in one location; this will reduce the number of URLs to keep track of, and more importantly provide system-specific SLA’s (because really, the personal sites don’t have the same uptime requirements as the payroll does).
Another note of interest (especially for larger organizations) is ensuring a Single Sign-On solution. Most people familiar with IIS and ASP.Net will immediately think of Active Directory, but a surprising number of solutions use their own system (such as SQL membership provider). One technology which has recently gained a lot of interest is Security Assertion Markup Language (SAML). This is a technology which is natively supported by SharePoint 2010, and can provide authentication against non-Microsoft systems such as Novell, Sun (now Oracle), or OpenLDAP. By ensuring a Single Sign-On solution, a SharePoint portal can provide an experience similar to that of tightly integrated systems, while staying isolated for maintenance.