As far as I can see (1) (2) (3) (4), the way JDK7 does it, is by calling GetFileInformationByHandle on the files and comparing dwVolumeSerialNumber, nFileIndexHigh and nFileIndexLow.
Per MSDN:
You can compare the VolumeSerialNumber and FileIndex members returned in the BY_HANDLE_FILE_INFORMATION structure to determine if two paths map to the same target; for example, you can compare two file paths and determine if they map to the same directory.
I do not think this function is wrapped by .NET, so you will have to use P/Invoke.
It might or might not work for network files. According to MSDN:
Depending on the underlying network components of the operating system and the type of server connected to, the GetFileInformationByHandle function may fail, return partial information, or full information for the given file.
A quick test shows that it works as expected (same values) with a symbolic link on a Linux system connected using SMB/Samba, but that it cannot detect that a file is the same when accessed using different shares that point to the same file (FileIndex is the same, but VolumeSerialNumber differs).
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