DIsclaimer: I'm from Seattle. I'm biased towards the green siren.
Mocha Joes is a great little coffee shop. Comfortable seating, check. Good coffee, check. Plenty of places to sit and study, check. Good music, check. But here's where Mocha Joe's stands head-and-shoulders above the rest: their food is unbelievable. They have a homemade soup sitting in a crock-pot ready for ordering almost every day. Their sandwiches are delicious and not too expensive. Their desserts and muffins are fresh.
Mocha Joe's gets all their breads from a local bakery. They get all their meats from high-quality sources. They make their soups made in-house. I think it would do them a service to change their name to a cafe, because that's where they shine. They also provide catering services to local businesses with sandwiches, salads, and soups.
Check it out, definitely. It comes highly recommended from me.