Well your accountant is correct, give her a raise...wait scratch that, accountants make far more than they deserve to begin with
The $3,000 limit is on capital losses in excess of capital gains, but you can sell your junk stocks to offset the capital gain on the sale of one of your homes (which is not, I presume, your primary residence) as much as you want, not to exceed $3,000 in losses above your capital gains amount.
So if you sold your house for $28,000 in capital gains you can sell your stocks and claim up to $31,000 in capital losses. Anything you sell that provides capital loss beyond that can not be claimed, but can be carried over to next year.