C# Signature:

[DllImport("wintrust.dll", ExactSpelling = true, SetLastError = false, CharSet = CharSet.Unicode)]
static extern WinVerifyTrustResult WinVerifyTrust(
     [In] IntPtr hwnd,
     [In] [MarshalAs(UnmanagedType.LPStruct)] Guid pgActionID,
     [In] WinTrustData pWVTData
);

VB Signature:

Declare Function WinVerifyTrust Lib "wintrust.dll" (TODO) As TODO

User-Defined Types:

namespace Security.WinTrust
{
    using System;
    using System.Runtime.InteropServices;

    #region WinTrustData struct field enums
    enum WinTrustDataUIChoice : uint
    {
        All = 1,
        None = 2,
        NoBad = 3,
        NoGood = 4
    }

    enum WinTrustDataRevocationChecks : uint
    {
        None = 0x00000000,
        WholeChain = 0x00000001
    }

    enum WinTrustDataChoice : uint
    {
        File = 1,
        Catalog = 2,
        Blob = 3,
        Signer = 4,
        Certificate = 5
    }

    enum WinTrustDataStateAction : uint
    {
        Ignore = 0x00000000,
        Verify = 0x00000001,
        Close = 0x00000002,
        AutoCache = 0x00000003,
        AutoCacheFlush = 0x00000004
    }

    [FlagsAttribute]
    enum WinTrustDataProvFlags : uint
    {
        UseIe4TrustFlag = 0x00000001,
        NoIe4ChainFlag = 0x00000002,
        NoPolicyUsageFlag = 0x00000004,
        RevocationCheckNone = 0x00000010,
        RevocationCheckEndCert = 0x00000020,
        RevocationCheckChain = 0x00000040,
        RevocationCheckChainExcludeRoot = 0x00000080,
        SaferFlag = 0x00000100,        // Used by software restriction policies. Should not be used.
        HashOnlyFlag = 0x00000200,
        UseDefaultOsverCheck = 0x00000400,
        LifetimeSigningFlag = 0x00000800,
        CacheOnlyUrlRetrieval = 0x00001000,      // affects CRL retrieval and AIA retrieval
        DisableMD2andMD4 = 0x00002000      // Win7 SP1+: Disallows use of MD2 or MD4 in the chain except for the root
    }

    enum WinTrustDataUIContext : uint
    {
        Execute = 0,
        Install = 1
    }
    #endregion

    #region WinTrust structures
    [StructLayout(LayoutKind.Sequential, CharSet = CharSet.Unicode)]
    class WinTrustFileInfo
    {
        UInt32 StructSize = (UInt32)Marshal.SizeOf(typeof(WinTrustFileInfo));
        IntPtr pszFilePath;                     // required, file name to be verified
        IntPtr hFile = IntPtr.Zero;             // optional, open handle to FilePath
        IntPtr pgKnownSubject = IntPtr.Zero;    // optional, subject type if it is known

        public WinTrustFileInfo(String _filePath)
        {
            pszFilePath = Marshal.StringToCoTaskMemAuto(_filePath);
        }
        ~WinTrustFileInfo()
        {
            Marshal.FreeCoTaskMem(pszFilePath);
        }            
    }

    [StructLayout(LayoutKind.Sequential, CharSet = CharSet.Unicode)]
    class WinTrustData
    {
        UInt32 StructSize = (UInt32)Marshal.SizeOf(typeof(WinTrustData));
        IntPtr PolicyCallbackData = IntPtr.Zero;
        IntPtr SIPClientData = IntPtr.Zero;
        // required: UI choice
        WinTrustDataUIChoice UIChoice = WinTrustDataUIChoice.None;
        // required: certificate revocation check options
        WinTrustDataRevocationChecks RevocationChecks = WinTrustDataRevocationChecks.None;
        // required: which structure is being passed in?
        WinTrustDataChoice UnionChoice = WinTrustDataChoice.File;
        // individual file
        IntPtr FileInfoPtr;
        WinTrustDataStateAction StateAction = WinTrustDataStateAction.Ignore;
        IntPtr StateData = IntPtr.Zero;
        String URLReference = null;
        WinTrustDataProvFlags ProvFlags = WinTrustDataProvFlags.RevocationCheckChainExcludeRoot;
        WinTrustDataUIContext UIContext = WinTrustDataUIContext.Execute;

        // constructor for silent WinTrustDataChoice.File check
        public WinTrustData(String _fileName)
        {
            // On Win7SP1+, don't allow MD2 or MD4 signatures
            if ((Environment.OSVersion.Version.Major > 6) ||
                ((Environment.OSVersion.Version.Major == 6) && (Environment.OSVersion.Version.Minor > 1)) ||
                ((Environment.OSVersion.Version.Major == 6) && (Environment.OSVersion.Version.Minor == 1) && !String.IsNullOrEmpty(Environment.OSVersion.ServicePack)))
            {
               ProvFlags |= WinTrustDataProvFlags.DisableMD2andMD4;
            }

            WinTrustFileInfo wtfiData = new WinTrustFileInfo(_fileName);
            FileInfoPtr = Marshal.AllocCoTaskMem(Marshal.SizeOf(typeof(WinTrustFileInfo)));
            Marshal.StructureToPtr(wtfiData, FileInfoPtr, false);
        }
        ~WinTrustData()
        {
            Marshal.FreeCoTaskMem(FileInfoPtr);
        }
    }
    #endregion

     enum WinVerifyTrustResult : uint
     {
         Success = 0,
         ProviderUnknown = 0x800b0001,           // Trust provider is not recognized on this system
         ActionUnknown = 0x800b0002,         // Trust provider does not support the specified action
         SubjectFormUnknown = 0x800b0003,        // Trust provider does not support the form specified for the subject
         SubjectNotTrusted = 0x800b0004,         // Subject failed the specified verification action
         FileNotSigned = 0x800B0100,         // TRUST_E_NOSIGNATURE - File was not signed
         SubjectExplicitlyDistrusted = 0x800B0111,   // Signer's certificate is in the Untrusted Publishers store
         SignatureOrFileCorrupt = 0x80096010,    // TRUST_E_BAD_DIGEST - file was probably corrupt
         SubjectCertExpired = 0x800B0101,        // CERT_E_EXPIRED - Signer's certificate was expired
         SubjectCertificateRevoked = 0x800B010C,     // CERT_E_REVOKED Subject's certificate was revoked
         UntrustedRoot = 0x800B0109          // CERT_E_UNTRUSTEDROOT - A certification chain processed correctly but terminated in a root certificate that is not trusted by the trust provider.
     }

    sealed class WinTrust
    {
        private static readonly IntPtr INVALID_HANDLE_VALUE = new IntPtr(-1);
        // GUID of the action to perform
        private const string WINTRUST_ACTION_GENERIC_VERIFY_V2 = "{00AAC56B-CD44-11d0-8CC2-00C04FC295EE}";

        [DllImport("wintrust.dll", ExactSpelling = true, SetLastError = false, CharSet = CharSet.Unicode)]
        static extern WinVerifyTrustResult WinVerifyTrust(
            [In] IntPtr hwnd,
            [In] [MarshalAs(UnmanagedType.LPStruct)] Guid pgActionID,
            [In] WinTrustData pWVTData
        );

        // call WinTrust.WinVerifyTrust() to check embedded file signature
        public static bool VerifyEmbeddedSignature(string fileName)
        {
            WinTrustData wtd = new WinTrustData(fileName);
            Guid guidAction = new Guid(WINTRUST_ACTION_GENERIC_VERIFY_V2);
            WinVerifyTrustResult result = WinVerifyTrust(INVALID_HANDLE_VALUE, guidAction, wtd);
            bool ret = (result == WinVerifyTrustResult.Success);
            return ret;
        }
        private WinTrust() { }
    }
}

Alternative Managed API:

CAPICOM [http://msdn2.microsoft.com/en-us/library/ms867087.aspx]

Notes:

I noted that under some cicumstances the destructors are called too early and memory is corrupted, therefore WinVerifyTrust returning FileNotSigned even if the file was actually signed. I recommend replacing the destructors with Dispose() and calling dispose at the end of VerifyEmbeddedSignature().

Tips & Tricks:

    static public bool CheckFile(string filename)
    {
        // check digital signature
        bool ret = WinTrust.VerifyEmbeddedSignature(filename);
        // do some other checks - for example verify the subject
        X509Certificate2 cert = new X509Certificate2(filename);
        return ret && cert.Verify() && cert.Subject == <CN=you, O=you,....>;
    }

Sample Code:

System.Console.WriteLine("Signature is OK: {0}", WinTrust.VerifyEmbeddedSignature(fileName));