I am trying to figure out where or how i should store application secrets and keys inside a desktop application.
For example a facebook app key or dropbox key and secret.<
For each user account generate a new access token for the application when they successfully log into your service. Your login service should be designed much like a login for a website:
This auth token provided by your API will only work for the individual account and as such should only allow the user to perform operations to their individual account. So for instance, if a user wants to perform an operation they must be able to provide a valid auth token in order to complete the action. Using this method attackers will still be able to obtain an auth key, but that auth key will only be able to perform operations for the account in which it is generated. It will not be able to perform operations on anyone else account. The idea here is to let them mess with data but to keep the bad activity compartmentalized to one account.
From there, if you do have generic API calls (say an image search) that accesses data from multiple accounts make sure that you are never returning or allowing for any account to access all the data in your system outright. Provide only a limited number of records. In this case the system is still performing its job, but at no point allows all the records in your system to be accessed.
I typically implement a service like this:
Using these methods you should be able to make a fully operational desktop application. There are outliers to this functionality, if you have any post them up in the comments and we can dive further into the problem and see if this solution can still work for you.