> Does it come with package management yet?
No. There is the Windows Store (all or most Metro apps, GUI) and things like NuGet for Visual Studio, but that's not what you're looking for. There are third-party solutions.
[EDIT: See sibling comments; W10 adds one.]
> Can I easily avoid DLL hell these days?
DLL Hell is no longer a concern. It's not a matter of avoiding it, it won't happen except perhaps in very unusual edge cases I'm not familiar with.
> Can I add my own local repository and use it to maintain a fleet of workstations, making sure they always have the same configuration no matter what?
You can do this. This is one reason Windows is so big in enterprise.
> Is it easily possible to connect to a Windows machine and administer it from a command line/scripting environment?
Yes.
> Can I disable the GUI and use Windows without tying up resources for unneeded functionality - i.e. no graphics card required?
In Server 2012 onwards, the GUI is optional.
> If its not onboard, can I validate that 3rd-party with signed keys? Is there an onboard key agent that will make this possible?
I am not 100% on what you want, but yes, Windows executables are commonly signed and that is integrated with the OS.
> Is there an easy way to get a compiler onboard without requiring registration and so on, or does it ship with development tools already set up and configured?
Windows does not ship with a compiler or other developer tools installed. You can install Visual Studio 2013 Community Edition, which has all the features of Professional Edition, for free and without registration (afaik - I'm doing it right now, so if I'm wrong, I'll edit). You can of course install all the free-software development tools you want. Most tools support Windows reasonably well.
> Are these tools usable without requiring GUI involvement - i.e. remotely?
Yes, although most people don't do so. I've only fiddled around. I've heard that manually fiddling with msbuild is actually more pleasant than using the GUI.