These booksellers are not perfect but they have much better records than many of their competitors. They:
Better World Books is a certified B-Corporation based in the US and sells both new and second hand books. It is a for-profit social enterprise and is committed to supporting literacy. Every time you purchase a book from Better World Books they donate a book to someone in need and they also give grants to non-profits and libraries for literacy projects.
Blackwell's is a UK based academic book seller with around 40 stores in addition to it's global online sales.
BOOKS etc is a UK online business that is based in Aldershot, Hampshire.
Bookshop.org is an online bookshop and is a B-Corporation with a mission to financially support local, independent bookshops. They give away over 75% of their profit margin to bookshops, publications, authors and others who make up the thriving, inspirational culture around books and you can choose to donate all the profit from the purchase of your book to your local bookshop.
ebooks is an independent ebook retailer that sells worldwide
Foyles has 7 bookshops across the UK and is now owned by Waterstones.
Hive is a UK based online book store that shares it's profies with independent high street book stores.
The Guardian Bookshop is the online bookshop for The Guardian and The Observer.
WHSmith is a UK based chain of newsagents