Following on from mrb's entry on the Salvation Army's Wanchai Family Store, I can confirm that their Stanley location also has an offering of books. It's a split level store, with the books being at the very back of the upper floor.
If you're coming off the buses to Stanley, as you walk down the taxi/pedestrian street towards the market, hang a right at the library as if you're walking to the restaurant/bar area along the bay, and you'll pass the store on the left not far past the library.
Here are the details from their site:
Stanley Family Store G/F, 98 Stanley Main Street, Stanley, Hong Kong Opening Hours:
(Tel:3197-0070)
http://www.salvation.org.hk/Services/Recycling/FamilyStoreTable(e).htm#wc