I've got a few programs for you:
For starters, I hope to see more options for the gui version of MediaInfo for GNU/Linux, as I find it to be surprisingly inferior to the same program for Windows, lacking many of the menus and options Windows users can enjoy (especially the option to use something other than the "easy" view by default).
Also, like Yojimbo197, I have yet to find a GNU/Linux disc burning program that measures up to ImgBurn. Brasero performs quite nicely, but lacks a number of features. Perhaps if ImgBurn were to become free or open sourced, a GNU/Linux fork would manifest itself.
I wish Adobe would continue making Flash Player for GNU/Linux systems as well. Likewise for Microsoft Silverlight. Oh, if only these programs were free!
Of course, all these programs can run on Wine, but that's not the point.