As far as I know, WHSmith sold out their ebook store to Kobo. The irritating thing about Kobo is that you can only buy one book at a time, and their customer service... requires improvement. But they are my second go-to ebook store after Amazon. They do money-off offers quite regularly. (And their book readers are nice.)

Waterstones - I think I've bought from them once, because that's the only time they had what I wanted at the cheapest price. Generally they either don't have what I want, or they have it but with a hefty price hike.

Generally, I have to admit, I buy from Amazon. It's cheap, it's easy, and the customer service is good.