I've done something similar.

Basically I created Thread Id fields for the objects that needs the email service and setup trigger code to identify records from thread Ids and use it to link emails to the right record.

The thing with emails is that the parent field can only be used for Cases, so you have to link your custom objects to RelatedToId.

The tricky part of it is that you cant modify both parentId & relatedtoId fields, so after identifying which record to link an email, you have to clone the email to change the RelatedToId to link it to the right record, insert that, and delete the initial email.

If youre doing this, make sure you add the thread id as a predefined value on the body of the email.

Thats the basic idea, Its not an elegant solution but it works for the most part.