Here are a few I like.
Amnesia, at Herengracht 113. Best all around place to hang and smoke. Great weed, great staff, great atmosphere.
Het Ballonnetje, at Roetersstraat 12. Ask for the fresh Super Polm.
The Old Church, at Oudekerksplein 54. I love to sit upstairs and stare out the window.
Two Twenty Two, at Oudezijds Voorburgwal 222. Great place if you love trance music. Try their Northern Lights Skuff!
Wow only ONE MORE? How can I choose just one more? There are so many good ones....
OK.
The Saint, at Regulierssteeg 1. This is my favorite place for hash cappuccino and Hash hot chocolate.
And Stix, at Utrechtsestraat 21. Try the 'homemade gunpowder'. Killer kif!
Sorry, I guess that was six.

Here are five I no longer spend my time in for various reasons.
Double Reggae
High Time
Hollywood
Monaco (closed anyway)
Central


What the hell, here's five more I like...
Greenhouse, all locations. Great selection.
De Dampkring, at Handboogstraat. Try the Buddah's Sister and Dutch Moonshine!
420/de Kuil, at Oudebrugsteeg 27. FZ Rules!
Pink Floyd, at Haarlemmerstraat 44. Excellent hash.
1e Hulp, at Marnixstraat 194. Chill place for lounging.
Blue Velvet, at Haarlemmerstraat 64. I love their cat!
Global Chillage, at Kerkstraat 51. Best wall art, and chillout music.

Plus all the ones mentioned in the above posts are great too.^^^
OOPS! That's more than five again. Oh well.
 Don't take anyone's word for which shop is 'best'. Go find your own favorite.

Have fun!
P.S. Start another thread to find out where to eat!