http://www.thesoftlanding.com/
great for BPA-, phthlate-free, etc. bottles, cups, teethers, pacifiers, etc.
http://www.ecobabybuys.com
you can sign up to receive an email each day for a discounted baby product
greenbabybargains.com
is another one with daily bargains
healthystuff.org
to make sure the car seats, toys, etc., that you plan to buy are lead-free, etc.
ewg.org
also check out the environmental working group's skin deep database to make sure you are buying cosmetics, baby wash, soaps, etc., that are made with safe ingredients
http://www.naturepedic.com/
I'd also recommend checking out this type of crib mattress
there are lots of other online stores (and a lot of stuff available at Amazon), such as babyearth.com... just check around for coupons and free shipping offers to help make it a bit more affordable! good luck!