For work, I’m running SharePoint 2007 with customizations to allow AJAX and custom .aspx applications. There have been some issues that aren’t readily documented.

The Application Event Log gives errors such as:
Error: Failure in loading assembly: Microsoft.SharePoint, Version=11.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c

and

Exception information:
Exception type: HttpParseException
Exception message: Could not load file or assembly ‘Microsoft.SharePoint.ApplicationPages, Version=12.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c’ or one of its dependencies. The system cannot find the file specified.

SOLUTION:
Some people claim putting the Microsoft.SharePoint.ApplicationPages.dll file (found in C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\CONFIG\BIN) into the GAC. This may or may not be necessary. I was able to fix it by opening the web.config file (pretty much any web.config file I could find) and find the configuration section. Inside the declaration tag, there’s a namespace defined: xmlns=”http://schemas.microsoft.com/.NetConfiguration/v2.0″. Remove that part of the declaration and everything works.

Note that you have to do this for the application as well as for the administrative web.config (find the exact directory by looking at the Home Directory tab of IIS for the administrative virtual directory). The administrative “missing” dll is located at C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\CONFIG\ADMINBIN\Microsoft.SharePoint.ApplicationPages.Administration.dll, which may or may not need to be put in the GAC).

For completeness, the GAC is the Global Assembly Cache, which is usually c:\windows\assembly.

As a separate problem, you may have trouble running search through SharePoint if you remove root from the managed paths section. This is clearly documented here: http://home.infusionblogs.com/kguenther/Lists/Posts/Post.aspx?ID=321