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
2009 - Enchantment of the Seas
2010 - Freedom of the Seas