Most of the non-candidate ads you've seen on your TV this year have been paid for by non-profit organizations that don't have to report their donors. I really do mean "most." As Andy Kroll points out, non-profits and business groups made up 91 percent of "independent expenditures" in the first part of 2012. The non-profits, like Crossroads GPS, the 60 Plus Association, and Americans for Prosperity, don't have to report the names of their donors. AFP can buy $6 million or so of TV time to tell voters about Solyndra, for example, and the people funding the ads can stay mysterious.
The FEC might have just complicated that. Its new statement in the ongoing Van Hollen v. FEC case (read Kroll above for the details, but it's basically a disclosure lawsuit)
Effective March 30, 2012, persons making disbursements for electioneering communications should report "the name and address of each donor who donated an amount aggregating $1,000 or more to the person making the disbursement, aggregating since the first day of the preceding calendar year."
That would mean transparency for anything the FEC's defined as a political ad. I've reached out to some 501(c)4 groups to determine what this means for them. There were no immediate answers, no "phew, we're safe" or "we're screwed" takes.