We decided to include the work item id in the email link. Not perfect but not really that bad either. One remaining problem involves the determination of the work item id when sending the email. Ideally the process would look something like this:
1) user initiates the registration
2) system sends a verification email
3) the process transitions to the human task, waiting for the user to follow the link, confirm the registration, etc.
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The problem is that we need to know the work item id for the human task in step 2, in order to include it in the email. But, the task is only created in step 3. The solution we found was to combine steps 2 and 3. We subclassed CommandBasedWSHumanTaskHandler and overrode the executeItem method to send the email right before proceeding with the human task. At that point the work item id is known and we can include it in the email. It works fine but feels a little awkward. If anyone has a more elegant solution, I'd love to hear it.
In any case, thanks for all the replies.
Tommer