How to generate Email-to-Case thread id inside template:
Generate the thread Id
public static String getThreadId(String caseId){
public static String getThreadId(String caseId){
return '[ ref:_'
+ UserInfo.getOrganizationId().left(5)
+ UserInfo.getOrganizationId().mid(11,4) + '._'
+ caseId.left(5)
+ caseId.mid(10,5) + ':ref ]';
}
Send customEmail and Add ThreadId
public void sendCustomEmail(User selectedUser, Contact selectedContact, String templateName, Map<String, String> customVariables){
EmailTemplate emailTemplate = [select Id, Subject, HtmlValue, Body from EmailTemplate where DeveloperName=:templateName];
if (selectedContact==null){
selectedContact = selectedUser.Contact;
}
String customSubject = emailTemplate.Subject;
if (customVariables.containsKey('joinContactName')){
customSubject = customSubject.replace('{!JointContactName}', customVariables.get('joinContactName'));
}
//Add ThreadId to the Subject
if (customVariables.containsKey('ThreadId')) {
customSubject = customSubject.replace('{!ThreadId}', customVariables.get('ThreadId'));
}
String htmlBody = emailTemplate.HtmlValue;
htmlBody = htmlBody.replace('{!Contact.FirstName}',selectedContact.FirstName);
htmlBody = htmlBody.replace('{!Contact.Email}', selectedContact.Email);
if (customVariables.containsKey('Link')){
htmlBody = htmlBody.replace('{!CustomUrl}', customVariables.get('Link'));
} else if (customVariables.containsKey('link')){
htmlBody = htmlBody.replace('{!CustomUrl}', customVariables.get('link'));
} else if (customVariables.containsKey('joinContactName')){
htmlBody = htmlBody.replace('{!JointContactName}', customVariables.get('joinContactName'));
}
//Add ThreadId to the htmlBody
if (customVariables.containsKey('ThreadId')){
htmlBody = htmlBody.replace('{!ThreadId}', customVariables.get('ThreadId'));
}
String plainBody = emailTemplate.Body;
plainBody = plainBody.replace('{!Contact.FirstName}',selectedContact.FirstName);
plainBody = plainBody.replace('{!Contact.Email}', selectedContact.Email);
if (customVariables.containsKey('Link')){
plainBody = plainBody.replace('{!CustomUrl}', customVariables.get('Link'));
} else if (customVariables.containsKey('link')){
plainBody = plainBody.replace('{!CustomUrl}', customVariables.get('link'));
} else if (customVariables.containsKey('joinContactName')){
plainBody = plainBody.replace('{!JointContactName}', customVariables.get('joinContactName'));
}
//Add the threadId to the plainBody
if (customVariables.containsKey('ThreadId')){
plainBody = plainBody.replace('{!ThreadId}', customVariables.get('ThreadId'));
}
Messaging.Singleemailmessage email = new Messaging.Singleemailmessage();
List<OrgWideEmailAddress> orgWideEmailAddress = [Select Id, Address from OrgWideEmailAddress where DisplayName=:ORGWIDEEMAILADDRESSNAME];
//Set ReplyTo as the Email-to-Case email address
if (customVariables.containsKey('ThreadId')){
List<EmailServicesAddress> emailServicesAddress = [SELECT Id,AuthorizedSenders,EmailDomainName,IsActive,LocalPart FROM EmailServicesAddress where IsActive=true and (LocalPart like '%service%' or LocalPart like '%support%')];
if (!emailServicesAddress.isEmpty()){
EmailServicesAddress emailToCase = emailServicesAddress.get(0);
email.setReplyTo(emailToCase.LocalPart +'@'+ emailToCase.EmailDomainName);
email.setSenderDisplayName('Client Support');
} else {
email.setReplyTo('customer-service@gmail.com');
email.setSenderDisplayName('Client Support');
}
}
email.setTargetObjectId(selectedContact.Id);
email.setSaveAsActivity(true);
email.setSubject(customSubject);
email.setHtmlBody(htmlBody);
email.setPlainTextBody(plainBody);
if (customVariables.containsKey('WhatId')){
email.setWhatId(customVariables.get('WhatId'));
}
Messaging.sendEmail(new Messaging.SingleEmailmessage[] {email});
}
Putting it all together
Map<String, String> mappingOfCaseFields = new Map<String, String>();
mappingOfCaseFields.put('ThreadId', App_Service.getThreadId(paymentCaseId));
App_Service.instance.sendCustomEmail(null, contact, 'App_Support_Template', mappingOfCaseFields);
Thys Michels Blog 
Hi Michel,
This Generate the thread Id will not work as expected for an org where the 5th character is non-zero.
++Prakash.
Yes, I am having the same scenario and the 5th character is non zero. Its not working for me. The better solution is to use formual field.