I think as far as coffee it depends on what you get and where you get it from. Example, on my last cruise, on the Enchantment, they had a specialty coffee house, Latte-tudes. If you got it from there, it would cost you.
In the case of the Freedom, depending upon what you get from the Cafe Promenade, it is my understanding that there are some items that are free and some that are not.
In the dining room, if you want coffee with your dessert, that is included and there is no extra charge for that.
2007 - Majesty of the Seas (Bahamas)
2009 - Enchantment of the Seas (Western Caribbean)
2010 - Freedom of the Seas (Western Caribbean)
2013 - Golden Princess (Alaska, roundtrip from Seattle)