Big ones:
-The aforementioned package repository/app store. Seriously, if you have used apt-get and have an iPhone/iPod Touch, it's probably stuck you as odd that this isn't already there. Especially when you go to downloads.apple.com, and note that the Apple Menu has an option called "Mac OS X Software" that takes you there. That option should fire up the graphical package manager, not take you to some page on Apple's site.
-ZFS, or something similar.
-Resolution independence
-64 bit Kernel should be the default with K32 as an option, not the other way around.
Little things:
-Cut and paste in the Finder
-Tabbed Finder (if you don't want to use it, you don't have to. Oh, and they should be spring loaded.)
-Tabs-on-top in Safari, Terminal, and Finder
-QuickLook in Stacks (you can already highlight with the arrow keys in Fan and Grid views, and the spacebar does nothing. It should QuickLook the highlighted file)
-Somebody else said an active application marker in the Dock. I like that idea. Maybe something simple, like a brighter or different color indicator dot.
-Whoever suggested closing windows in Expose like you can close widgets, I like that idea too
-Kill the white border on the 2D Dock, Grid view, and Dock menus, or at least make it thinner.
-Make the 2D Dock the default, even on the bottom. Maybe keep the shelf effect, but the mirror-look is just tacky, and the indicators are hard to see.
-Add the "frosted" effect to the 2D Dock and fix the opacity/brightness, so it matches the Dock Menus and Stack Grids.
-Switch the Keychain to AES-256, for that last layer of security and e-peen.