When hosting a WCF service in IIS 7 on my 64-bit Windows 2008 machine I got the following error:
System.BadImageFormatException: Could not load file or assembly 'APToolkitNET' or one of its dependencies. An attempt was made to load a program with an incorrect format.
To resolve this I had to set the "Enable 32-Bit Applications" ([enable32BitAppOnWin64]) to true on the applicable application pool.
See also:

I've also run into the same issue with the Application Pool for a Sitecore CMS 6 install.
Server Error in '/' Application.
Could not load file or assembly 'System.Data.SQLite, Version=1.0.48.0, Culture=neutral, PublicKeyToken=db937bc2d44ff139' or one of its dependencies. An attempt was made to load a program with an incorrect format.
Description: An unhandled exception occurred during the execution of the current web request. Please review the stack trace for more information about the error and where it originated in the code.Exception Details: System.BadImageFormatException: Could not load file or assembly 'System.Data.SQLite, Version=1.0.48.0, Culture=neutral, PublicKeyToken=db937bc2d44ff139' or one of its dependencies. An attempt was made to load a program with an incorrect format.