Артем

Если значения действительно разные, отсортированные по возрастанию и размер у них 4 байта:

var stream1 = new BinaryReader(File.OpenRead("someFile1.bin"));
var stream2 = new BinaryReader(File.OpenRead("someFile2.bin"));
var output = new BinaryWriter(File.OpenWrite("output.bin"));

if (stream1.PeekChar() != -1 && stream2.PeekChar() != -1)
{
    var val1 = stream1.ReadInt32();
    var val2 = stream2.ReadInt32();

    while (true)
    {
        if (val1 == val2)
        {
            output.Write(val1);

            if (stream1.PeekChar() == -1 || stream2.PeekChar() == -1) break;
            val1 = stream1.ReadInt32();
            val2 = stream2.ReadInt32();
        }
        else if (val1 < val2)
        {
            if (stream1.PeekChar() == -1) break;
            val1 = stream1.ReadInt32();
        }
        else
        {
            if (stream2.PeekChar() == -1) break;
            val2 = stream2.ReadInt32();
        }
    }
}

stream1.Close();
stream2.Close();
output.Close();