Two I can't believe aren't mentioned yet;
ReTargettable Graphics/Audio : Sure, in most OS now you can pick a full screen resolution for a game. Of course, the Amiga did it first, and took it further, also allowing you to pick which video card you use, and which rendering mode, and also being able to choose differing sound cards.
These were certainly good but they were basically third party extensions that have come to be a part of most serious user's OS installs. Their very existence, however, exposes a weakness in the OS in that the concept should really have been thought of by the OS designers rather than hardware vendors and the like.
ARexx : A single scripting language that allows you to create interactions between any major software packages you happen to have. If only modern PC, Mac or Linux applications got along this well, think of what we could do.......
Definitely a +1 for this, too.
Regarding linux, scripting is well served by shell script, Perl and more recently Python. Of course, what none of these have is the basic notion of "application hosts" which is what made (A)Rexx special on the Amiga, rather than the language itself.
I actually always thought Javascript (with importable application interfaces) would make a nice scripting system, but I am a curly brace whore.