These stand out and they are within an easy walk from each other in the Singel/Herengracht area.
1) Greenhouse Lounge (Haarlemmerstraat 64) (Former Blue Velvet)
http://www.coffeeshop.freeuk.com/BlueVelvet.html
Unique in so many ways, when you walk in and look at the floor you realize you are walking on the glass top of a huge aquarium. In addition to the usual benefits of the Greenhouse family this place has a truly outstanding kitchen, really great food, breakfast, salads, sandwiches, steaks… when I ordered an espresso it was delivered in a proper demitasse with a side glass of water, when I remarked to the cute waitress that I was impressed she said they receive barista training. The neighborhood is a great constellation of restaurants, shops, and great spots for people watching.
2) Siberie (Brouwersgracht 11)
http://www.coffeeshopsiberie.nl/eng/
http://www.coffeeshop.freeuk.com/Siberie.html
No food but definitely has a great tea collection. They also have poetry night, chess tournaments, and sometimes a dj. Very cool and laid back with a great friendly staff.
3) Amnesia (Herengracht 133)
http://www.coffeeshop.freeuk.com/Amnesia.html
The new remodel looks beautiful, more comfortable seating, enjoy the usual benefits of this great coffeeshop. Must try their fantastic mint lemonade!
One could start at the Greenhouse, go check out Siberie, walk around the Singel to see what's happening, then go to Amnesia… then backtrack to Greenhouse. Life is great!
And if you are hungry and gets to be dinner time De Belhamel restaurant is right there where the Herengracht and Brouwersgracht meet. If it is warm you can sit outside, or, try sitting by the windows overlooking the canals.
http://www.belhamel.nl/