I find Bonus is always so frustratingly chaotic that I can't deal with it! The ones near where I live are full of tourists, the one on Grandi is jammed with families, and the layout of the places seem to encourage traffic jams. The only reason I go there now is because they've got small avocados in string bags that are the most consistently ripe and delicious of any avocados I've found in Iceland.
Kronan is similarly priced but has a much wider range of produce and is a much better store layout. Plus, I ran into the mayor shopping there yesterday
Melabúðin is a tiny shop but such a treat to visit because they have the most amazing international products and cheeses, and a great meat/fish counter. Plus, it's nicely neighborhoody and has excellent service if you're looking for some odd product.
and finally Nóatún is open 24h (as are some Hagkaup locations) and is my go-to if I can't find something in the other usual shops.
For my organic needs and black beans (why are these so hard to find?) I go to Maður Lifandi or Yggdrasil.
Malls.. there are only 2 and I generally prefer Kringlan over Smaralind.
boutiques are mostly in one spot, on Laugavegur. However, I almost never buy my clothing basics in Iceland. The value for money is terrible here compared to my homeland favorites like TJ Maxx or Filene's Basement.