When you try to open a SharePoint site from SharePoint Designer and you receive this error:
The Web server at does not appear to have Microsoft SharePoint Foundation installed

Microsoft suggests doing the follow (did not work in my case)

To resolve this problem, enable the client integration. To do this, follow these steps:
Start SharePoint 2010 Central Administration, and then click Security.
Click Specify authentication providers.
If the Web application in the Web Application list is not the same application that you want to open in SharePoint Designer 2010, click Web Application on the Change Web Application list.
On the Select Web Application page, click the name of the Web application that you want to open.
Under Zone, Click Default to open the Edit Authentication page.
Under Enable Client Integration, click Yes, and then click Save.

In my case, it turned out that my web.config file was out of wack.
Only one of my web apps would fail to load in SharePoint Designer, all the other Web Apps / sites would load.
Opened a working and the non-working sites web.configs in NotePad++ and did a file compare.
Located the difference in the file and removed it.
For good housekeeping, i then fired off an IISreset.
*things to note, make sure you have a backup copy of your web.config file and this work was done in my Develop environment.)