Balto / Federal Hill / good coffee
Hang in there, Jamie D... what you're looking for doesn't exist yet, but watch for the FED opening in the spring. It's a new coffee house/ grill soon to be in the old McCrory's spot on Light Street, but they haven't started renovating the space yet. Initial reports are that they'll be open late nights and will not close at all between Friday morning and Sunday night.
Spoon's closes relatively early (6 or 7 ish I think).
If I interpret your request correctly, you are looking for a decent coffee shop with a trained and talented barista (a good indy)? Doesn't exist in Baltimore. The closest you will get is Jay Caragay's place, but he recently closed his Jay's Shaved Ice location (just for the winter I hope) and is only operating a kiosk in the Towson Library. To give you an idea, there aren't any places that I know of that use Intelligensia or Counter Culture.
If you are able to find a decent barista, let me know. I am so sick of dreck espresso topped with dish water foam that I now almost exclusively drink espresso at home.
Metropolitan on Charles Street is probably your best best in that area and at that time. They are more of a coffee house during the day and a restaurant at night, but they still have an espresso machine or coffee at all times and decent seating upstairs. Just don't expect much from their baristas.