If I sold off some of these stocks before year's end, I read somewhere that I could claim $3,000 of the loss against ordinary income. Is that correct? There is also something about carrying over additional loss to subsequent years, but probably no real advantage to selling all shares of both now.

First you net all your Schedule D transactions, including mutual fund cap gain distributions. If the bottom line is a loss you can apply $3,000 to that year's return, carrying forward any excess to the following year's Schedule D, where the process repeats.

I usually do my own taxes using Turbotax, would the process be too involved for me to handle this myself in 2009?

No.

Phil