I\'m using a website as a frontend and all users are authenticated with the standard ASP.NET Membership-Provider. Passwords are saved \"hashed\" within a SQL-Database.
It's been some time since I've tinkered with ASP.Net membership, but do remember dealing with something a bit related to it (needed to customize things due to an existing database of users). In that effort I overrode the methods (the existing user db had md5 hashed pwds).
So in the same "line of thought":
Expose the Membership API via a web service that your desktop app can reference. This way, you're not "re-creating" things, you're re-using them. You don't have to override anything, you're just exposing the existing methods via a web service for your desktop app.
Goes without saying that you'd have to secure this endpoint....
If the above is too sketchy for your taste, here's a link to the asp.net forums regarding some attempts to recreate the hashing....I can't confirm the accuracy, but it should be easy to test it out:
http://forums.asp.net/p/1336657/2899172.aspx