Nordstrom (half and half online and B&M)
Loft/AT (mostly online)
Kohl's (mostly underpinnings & sleepwear, IRL)
ON/Gap/BR/BR Outlet (all but last mostly online)
then probably a tie between Dress Barn, Garnet Hill, Lands' End, Talbots, Lord & Taylor (online), Eddie Bauer, and JC Penney.
I'm not sure how to count Amazon - I've started ordering clothes/shoes from them, but I never start there to search, it's just that I opt for them when they have the lowest price on a brand I buy. Especially shoes - I've found much better deals on Amazon for shoes recently than at Zappos, which I used to shop all the time and I haven't much this year.
The online/B&M distinction is a factor, too. There are some stores that are only online/catalog, of course (Lands' End, Garnet Hill, Boden). There are some stores that only carry my size/length online even though they have B&M stores (Loft, Gap) and I only go into the stores to return online orders or on impulse because I'm at the mall. Then there are stores I never shop online and only in person - Dress Barn, Kohl's, DSW, and for some reason Talbots - I look at their stuff online and like it, but never seem to pull the trigger, but in person it's much more dynamic and appealing.