In 2005, Microsoft started the anti-piracy initiative called Genuine Advantage. To be able to download from Microsoft Download Center, you would have had to pass the validation. It was the first time that Microsoft acknowledged the existence of Wine, by blocking its access to the downloads if a Wine specific registry key was found by the ActiveX control or their standalone tool.
These are some ways to detect Wine:
Check for the existence of "SOFTWARE\Wine\Wine\Config"
Presence of Wine specific API exports
wine_get_version in ntdll.dll (https://www.winehq.org/pipermail/wine-devel/2008-September/069387.html)
On a normal Windows system there will always be some specific processes running like csrss.exe (Client/Server Runtime Subsystem), dwm.exe (Desktop Window Manager), explorer.exe (File Explorer) and winlogon.exe (Winlogon). Some of those exes are just present in a specific range of Windows versions, so you have to consider those when checking for their presence. Not having them present could also mean that your application is running on a newer Windows that does not use them anymore. A normal Windows should generally speaking have more then 10 processes running, even if you don't have any programs running and under a non administrator account that does not allow you to view the list of running system processes. Having not much processes could as well mean that your program is running inside a sandbox.
Missing API functions or functionality
When you search for "unsupported" in the Wine source you will find easily places that have been identified to miss functionality to behave exactly like Windows. The file dlls\ntdll\om.c contains the API NtQueryObject and by looking at the code it sesms like it is missing support for some values in the main switch. This API is not officially documented by Microsoft but...
The API entry code generated by gcc will be different than the one that Microsoft Visual Studio compiler generates.
The Wine dll files are compiled different than the native Windows ones, there is another number of PE sections in files like kernel32.dll