in addition to all the spots mentioned id definitely check out re-up off of comm ave.  it's not as popular as bodega but they have a really solid clothing selection and if they got their shit together they have both an sb and jordan account.  awol in allston is another decent spot, recently renovated, decent clothes, much better selection on shoes, a lot of stuff you won't find at other spots from supra, creative rec, vans, etc.
underground hip hop is a must if you like hip hop at all, they'll have any album you've never been able to find or could ever want, real good selection of hip hop orientated clothes too.
hmm, what else, karmaloop is having a sale right now and that's all ive really got.