What we did may differ slightly from what you are trying to do, so what I describe below is what we did rather than specific advice about what you should do - hopefully you should be able to fill in the gaps!

Let me start by explaining the user's experience. 

The user wants to update a record (I'm describing update but this applies to insert as well). He updates a field to a value that we determine may not be valid by looking up against an object in a trigger. When the user clicks save, they are presented with a warning at the top of the screen, with an instruction that if they still want to proceed, there is a checkbox they can check. The user checks the checkbox and clicks save again. The record is saved without warning.

The cause of your problem is that there's no way of warning a user and letting them decide to do it anyway. You can only prevent the action from happening (addError()) or you can let it happen with no warning. The checkbox method I've described above kind of combines these two options. You use the addError to inform the user (of a duplicate in your case); you then use a checkbox to let them ignore the error.

I can't post our code here, but here's soem psuedo-code.

As it is (in your case), we have some logic that checks to see if there's a duplicate - if there is, we report an error. Presumably this is in a trigger and looks something like:

boolean hasDuplicate = checkForDuplicate();

if(hasDuplicate) {

      object.addError('It looks like the object your inserting is already in the database');

}

So the user tries to insert a duplicate and is stopped from doing it. Let's say there is now a checkbox on the object called Override__c. If the user has checked this box, we let them perform the operation i.e. we do NOT add the error. Pesudo-code:

if(object.Override__c == false && hasDuplicate) {

      object.addError('It looks like the object your inserting is already in the database. If you want to insert it anyway, check the "Override" box and click Save again.');

}

In this case, if that box is checked, the first part of the if statement is false and so the addError is not executed. Notice we've updated the error message as well.

One other thing with this method: when the object is saved, the value of Override will be saved along with it, so if the box has been checked, it will be stored as true in the database. If someone views or edits the record, they will not be warned. Maybe this is OK in your case, if it's not you need a way of setting the checkbox back to false. You can do this at the end of your trigger by updating all the objects checkboxes to false (or similar).

What we did was to do it in the before trigger, as in before triggers you can change the value of fields. To do that in an after trigger requires a database operation. Our problem was that we needed the value of the field in an after trigger; if we set it to false in the before trigger, the after trigger is always going to read the value as false! The way we got around this was to use a static map of booleans keyed by the ID of the object they relate to. In the before trigger we store the value of the field against the ID of the object; we then set it to fals and in the after trigger we use the static map variable.

Make sense? I hope so :)

Thinking out loud: I think it may be possible to use an s-control to do what you need, but I don't know s-controls and javascript well enough to specify how. Basically, on clicking the save button, present a dialogue box with a warning and "OK" and "Cancel" buttons. If the user clicks OK, perform the operation; if not don't. You'd need a method to call from the javascript to check for duplicates; depending on the response you'd present the dialogue box or not. You'd need to then handle the users decision and save/not save accordingly.

Hope that helps.