The atomic logo isn't a tile but an animation. There IS a program that can unpack the animation into pcx files, but I don't remember if it's official (and located on your Duke cd) or not.
And the midi's are (apart from the music dir on your cd, if I'm not mistaken) included in your grp file (duke3d.grp). Extract them with kextract.exe (located on your cd) by typing
kextract duke3d.grp *.mid (meaning every file with the .mid extension) in your dos prompt. (or use some fancy grp editor but I'm doing fine without one, thank you
)