When it comes to networking with Windows systems, since OS X 10.2 "Jaguar," Apple has relied on the open source "Samba" suite, which can be turned on in OS X's Sharing system preferences to allow for both file sharing and interaction with directory services from NT domains. While there are a few proprietary Windows file-sharing solutions for OS X, Apple's implementation of Samba has been welcome because of the package's open-source nature; however, sooner or later all things must come to an end.
Recently the Samba team changed the licensing for the software to the GPLv3 license, which adds a number of restrictions to the software that Apple has decided will not work for it. One likely feature is the GPLv3's crackdown on "Tivoization," which is where a company includes free software in commercial products but then restricts it from being modified by the end user (or at least implements it in such a way that tampering would result in the product not working correctly).
Because of these new restrictions, Apple will not be including Samba in future versions of OS X, though Samba will likely remain as an option to download, compile, and install in OS X for those who wish to use it.
Despite the lack of Samba, Apple's systems will still continue to work with Windows networks right out of the box. According to AppleInsider, Apple is apparently tackling the problem by building its own services for Windows networking, which will be included in the Server and Client variants of OS X Lion.
The changes users can likely expect from this are the end of support for NT domains in OS X, though even Microsoft has moved on from this technology in Windows 7. In addition, an Apple-supplied solution may also mean more-compatible networking between Windows and OS X, since Apple will be able to better customize its networking solutions into OS X.
As has been Apple's strategy in the past, we expect that Apple will start with a relatively bland and basic implementation of its networking solution, and over time work in more features as they mature. There may be a few setbacks at first, but overall it should keep similar functionality to what Samba can currently do.
Only time will tell what the exact changes will be for the end user, and more details may emerge as Lion matures, but be assured that it is highly unlikely Apple will drop support for Windows networking altogether.
Keep in mind, however, that along with Apple's use of Samba being affected by the new licensing, there may be other software that eventually could also suffer a similar fate. Apple currently includes a number of open-source packages besides Samba such as X11, ruby, python, and numerous command-line tools that could all upgrade to or implement the GLPv3 license and likewise be affected.