The things I miss from my Amigas today (I'm slowly getting things set up again - got a Minimig, and have an AROS install on my laptop, planning on getting a SAM or X1000) are mostly about hackability and elegance.
The platform as a whole, including the OS was so open / well documented, while still being a "proper" OS.
The things I regularly whine about missing on Linux (and OS X/ Windows) to anyone that cares to listen includes:
* Responsiveness.. I've never once used an OS since I gave up my last Amiga that's been remotely as responsive to user input.
* Modularity. The simplicity of writing device drivers, file systems, replacing system functionality.
* Arexx ports. I detest Arexx the language, but having ports for every major app is such a major thing.
* Ability for apps to open screens.
* No per-application window menus.
* Tight GUI integration. On Linux and everywhere else I'm a devoted shell / cli user. AmigaOS is the only OS I've used where I feel comfortable using the GUI most of the time.
* Datatypes (yeah, they need an upgrade / face lift, but anyway)
* Draggable screens (not entirely true - Enlightenment window manager supports it on Linux, and my current Ubuntu install is "close enough" with very smooth desktop switching... finally)
That's where most of the magic is for me today. Lots of nostalgia too. But the above are things I *still* want and that I'm not getting in other OS's.