Square Enix ordered the WindowerXIV team to cease and desist.
If you planned on using the Windower tool to play Final Fantasy XIV, then you might be in for a wait. The WindowerXIV site was shut down indefinitely after the site's owners received a cease and desist letter issued by Square Enix.
A statement on Windowerxiv.com says a new windower is in the works that won't be tied specifically to FFXIV. Rather, the new windower will work with every DirectX 9 and 10 game and contain "a powerful plugin interface with Windows XP support." Square Enix is well known for protecting its intellectual properties, and presumably the new windower wouldn't infringe upon the gaming companies trademarked products.
The windower tool has been used by countless players in Final Fantasy XI, partially because the game existed for years before Square Enix added a windowed mode.
However, the use of windower has always been a lightning rod of debate for FFXI players. Many have said the windower tool significantly enhanced their gaming experiences. Others criticize windower for being a third party tool capable of providing numerous advantages that are not available to other players. The FFXI terms of service strictly prohibits the use of third-party tools, but Square Enix was never known to ban anyone for using the tool.
Perhaps the news about the FFXIV windower is evidence of where Square Enix plans to stand on the issue from now on.