Come for the store hours, stay for the chocolate cakes and sugar-friendly specialty lattes. A note on the latter: if you are a ~coffee snob~ or espresso enthusiast, I don't know if I would necessarily point you to Michelangelo's. I would, however, if you are in the mood for an iced mocha or vanilla latte.
Anyway, Michelangelo's is where I go when I'm either too lazy to trek all the way to the Square for coffee (in my typical effort of trying to avoid State Street prices) or am in need of a coffee shop that stays open past 9 pm. That's right, at this point in time they have the latest hours of any coffee place in Madison.
The line is never long (unless it's a Saturday but that seems obvious) and seating is easy to find considering Michelangelo's has two large rooms with various seating indoors and a handful of tables outside for parties of two. Other than a few tables in the back of the shop, seating is meant for parties of one or two. The tables are small so plan accordingly.
As a fun rumor that I'm pretty sure is true, the owners of Michelangelo's are also the owners of Fair Trade Coffee at the lower end of State Street. Their baked goods and atmosphere are the same. That said, I personally think Michelangelo's has a better atmosphere.