Ai, too much to list. Modern Urban Guides has great listings on indie boutiques:
http://www.elephantshoeconcepts.com/
I'll go by neighborhood.
Main St (from just north of Broadway up until about 30th Ave
Jonathan + Olivia (Hanii Y, Development, Mike & Chris, Cheap Monday, F-Troupe shoes, Vanessa Bruno, Vince, karen walker, Earnest Sewn, Filippa K, Bulga, Spring&Clifton, Seven, Rag & Bone, United Bamboo, Whyred, Lewis Cho, Norma Kamali, much more. mens and Womenswear)
Eugene Choo
Front & Co (great consignment)
The Barefoot Contessa (pretty, girly dresses, tops and bottoms, gifts, accessories, jewelry)
Lark (one-stop-shop for Nudie and Denimbirds jeans, Sinbi, Bertoni, Petit Oiseau, Kulpa, Lark in-house brand, much more)
Motherland
Pleasant Girl
Burcu's Angels
Hotbox Accessories
Ark
...Um, I could go on.
Yaletown:
Vasanji, Atomic Model, Global Atomic, Bionic Footwear, Lola Home and Apparel, Basquiat, Eve, Babe Belangere Boutique, Mandula, Fine Finds
Gastown:
Komakino, Richard Kidd, One of a Few, Obakki, Woo Vintage, Dream, The Block, Mintage, Dutil, Subdivision, Hunt & Gather, Goon Pack
W 4th:
Gravity Pope! (aka shoe heaven), Liquid, Skyler, much more but I can't remember right now.
Commercial Drive:
Spank, Beckwomans, Little Miss Vintage, My Sisters' Closet, Kalena;s, Mintage, Retro Rock Vintage, Virgin Mary's, Riot
South Granville (south of Broadway

Misch, Boboli, Babs Studio Boutique, Ellis, Zebraclub, DKNY, Cattiva
Downtown:
Betsey Johnson, LV, Hermes, Used Vintage, Spank, Holt Renfrew, Wolford, Ports 1961, American Apparel, Fluevog, Winners, BEDO, Puma, Gsus, Tiffany, much more around Granville St and Burrard St, and all down Robson.
West Broadway:
Shine, Plenty, Loulou, Loulou Luv
visit my blog for more. (it's linked in my signature)