You would need to build the console application against the client that we be used to connect to the database. If you're using SDE 10.0 I would think that this would mean your client would need to be Desktop or Engine 10.0 or higher.
I don't know your particular business requirements, but if you're focused on data extraction it may be easier to write a python script to accomplish this task and run it as a scheduled task. The ArcObjects code shouldn't be too difficult to write based on the information you've provided so far. I would think that if I had to write this I would spend the bulk of my time on the joining data portion.