Not sure if this has already been mentioned, but there's one in particuluar that I find extremely convenient.
The way Amiga mounts devices and filesystems.
I say that, because I recently purchased a netbook pre-installed with windows 7. This wasn't going to fly well with me, though I do need a modern Windows OS to run stuff for school, but I downloaded Ubuntu and installed that instead. Ubuntu instists on EXT filesystems for the root partition (doensn't care what anything else is), as Amiga prefers FFS/SFS/whatever (though I probably could get a os3.1> on a fat32 if I really wanted). This is all fine and good, but I can't access the partition via windows, which insists on ONLY using fat/ntfs stuff. On the Amiga, I had little to no trouble mounting whatever filesystem I wanted with whatever device I wanted it on, because of the mountlist and dosdriver system, which I also find extremely more intuitive than the way Linux does things. (That could just be because I'm not used to it yet)
As for 2 other ideas, I'd have to run with the ability to boot w/o startup-sequence, and the multitasking. (Both mentioned already)
