"Should I sell stock and realize a gain before the end of the year to offset the remaining 6k loss to avoid being taxed on this gain when I sell it in the future?"
I don't necessarily recommend making investment decisions solely on the tax implications. Yes, you could realize a gain of up to $9000 and it would be tax-free, offset by the loss. But do you want to sell your positions if not for the tax implications? Do you need the money for spending, or would you invest in something else and would that investment be as good?
As long as you had a gain, you can re-buy the same investment without running into special rules, except that you will reset the holding period. By re-buying the investment, you will have a higher cost basis and pay less tax in the future, assuming it continues to gain value.
Alternatively, you can simply invest as seems best to you, take the $3000 against your other income, and carry the loss forward. Maybe you will have gains next year to offset the loss, or you can carry the loss forward until it is used. up.
