EmailMessages.getFormattedThreadingToken() returns the email threading token that is formatted with the correct prefix and suffix which is used in the Salesforce Email-To-Case threading. The returned token can be added to the Email Subject or Body so that when the users respond back, it will link the Email Message to the respective Case record in Salesforce.

Sample Apex Code:

/* START */
Id caseId = '500au00000560goAAA';
String formattedToken = EmailMessages.getFormattedThreadingToken(
	caseId
);
Messaging.SingleEmailMessage emailMsg = new Messaging.SingleEmailMessage();
emailMsg.setToAddresses(
	new String[] { '<EmailAddress>' }
);
emailMsg.setPlainTextBody(
	'Test Email Notification' 
	+ '\n\n' 
	+ formattedToken
);
emailMsg.setWhatId( 
    caseId 
);
EmailMessage latestIncomingEmail = [
    SELECT ReplyToEmailMessageId, Subject 
    FROM EmailMessage
    WHERE ParentId =: caseId
    AND Incoming = true
    ORDER BY CreatedDate DESC 
    LIMIT 1
];
emailMsg.setSubject( 
    latestIncomingEmail.Subject 
);
emailMsg.setInReplyTo(
    latestIncomingEmail.ReplyToEmailMessageId
);
OrgWideEmailAddress[] listOWEAs = [
    SELECT Id 
    FROM OrgWideEmailAddress 
    WHERE Address = '<OrgWideEmailAddress>'
];
Messaging.SingleEmailMessage mail = new Messaging.SingleEmailMessage();
if ( listOWEAs.size() > 0 ) {
    emailMsg.setOrgWideEmailAddressId(
        listOWEAs.get(0).Id
    );
}
Messaging.sendEmail(
    new Messaging.SingleEmailMessage[] { emailMsg }
);
/* END */

Here, EmailAddress is the Case Contact Email Address and OrgWideEmailAddress should be the Email Address where the Emails are getting forwarded to the Email-To-Case Service Email Address. So, the Email Address which forwards all the incoming emails to the Salesforce Email-To-Case Service Email Address should be added and verified in the Organization-Wide Addresses.