I would like to add a Note Log capability to my custom work item type.  It would work like the history field, but without showing th field changes: a user would type in a note - saving the work item appends it (along with user and datetime info) to the MyCompany.ChangeRequest.NoteLog reference field for display. 

It looked to me like using the History field type for the MyCompany.ChangeRequest.NoteLog reference field would do the trick, as in the MSDN "Field Type" article the history field is described as follows:

History   Use a History field for discussion threads and for keeping track of other historical information.

However, in the PTE (which I am using to do most of my customization) I am not allowed to associate a history field type to any reference field apart from System.History. 

My questions are:

• Is this a limitation of the PTE (can I achieve this by editing the raw XML instead?)
• If not, can someone suggest how I might replicate this functionality

Yes, custom fields cannot be of history type. Also, conversation control (history control) can only be associated with history field. It is because there is special way of storing data in history and processing it. Actually adding history does cause a revision. You can use long text fields to achieve users adding additional notes, but the experience won't be like history control.

If you are willing to get users to upgrade to SP1 beta & are willing to deploy custom controls to users, you can build your own custom control to achieve this rich functionality. Custom control documentation is at: http://blogs.msdn.com/narend/archive/2006/10/02/How-to-use-Custom-Controls-in-Work-Item-Form.aspx