According to Scott Rouse in some old threads in the legality forum he said that pdfs will need to be taken offline if they still bear the d20 logo, but that it may be as simple as modifying the pdf to cover the logo to be OK for sale. (OGL products that do not use the d20 STL are not impacted by the termination of the d20 STL).
I do not believe he specifically addressed the non logo parts of the d20 STL that entered into products (using specified references to trademarked names, etc.) however.
A couple companies have said they do not plan to put in the work to change their pdfs and will be retiring the ones with the logo (Adamant and Mongoose have said so). Others have already removed the logo from many of their pdfs (Bastion Press/Dragonwing Games, Fiery Dragon).
As far as I know WotC has not said what they plan to do with the 3e WotC pdfs. They are not subject to the terms of the d20 STL as WotC holds the d20 trademark and did not release them under the d20 STL. They could stay up forever for WotC to keep earning money from them or be taken down tomorrow so they do not "compete" with 4e stuff. They are currently full print cover price for the pdfs while pre3e ones range from $4-$6 each.