I am looking for Windows applications guidelines, related to configuration, log files and other issues not related to user experience - like
Thanks
A good point to start is the Windows 7 Logo Requirements, which define the requirements to qualify for the Windows 7 logo.
The folders to be used are for instance defined in point 2 of the Technical Requirements ("Install to the correct folders by default" with exact information about what to put where).
Read the Windows 7 Client Software Logo Program Documentation. http://download.microsoft.com/download/1/E/9/1E9580D9-2B2B-499C-918A-C9BA5EAC4A32/Windows%207%20Client%20Software%20Logo.pdf
The purpose of this document is to outline the technical requirements and eligibility qualifications an application must meet in order to participate in the Windows 7 Client Software Logo Program. The Windows platform has a broad ecosystem of products and partners that supports the platform. Displaying the Windows logo on your product represents a relationship and a shared commitment to quality between Microsoft and your company. Customers trust that seeing the Windows brand on your product ensures that it meets compatibility standards and performs well on the Windows platform. The Windows 7 Client Software Logo Program is made up of policies and technical requirements to help ensure that third-party applications carrying the Windows brand are both easy to install and reliable on PCs running Windows 7. End users and customers value stability, reliability, performance, and quality in the systems they purchase. Microsoft focuses some of its investments to meet these requirements for software applications designed to run on the Windows 7 platform for PCs. These efforts include compatibility tests for ease-of-use, better performance, and enhanced security on PCs running Windows 7 software. Microsoft compatibility tests have been designed in collaboration with industry partners and are continuously improved in response to industry developments and consumer demand.