I've found Urban Renewals in Allston to have great used baby clothing. I bought most of my son's clothes here, and no one ever knew they were used. No stains, very little fading. Each piece of clothing was only a couple dollars. It was often cheaper than yard sale prices and there is a huge variety.

They also have a furniture room on the side that has some used baby furniture. I can't vouch for the quality of those items though.