Specific examples are hard to come by, but I've noticed the general trend that differentiates the "good" from the "barely usable"..
* Scalability. For example, a good interface will pop up a "search" box for finding a security group in Active Directory. A bad one will let me chose security groups from a list or a drop-down. Both look equally good when the developer is working in a test environment. The latter will crash when used in a million-object directory. Similarly, check out the DNS management dialog box in Windows, or some Oracle tools. Both will show you "all" objects up to some limit (e.g.: 5000), but then provide a filter option to allow you to narrow down the "search" to prevent the GUI from melting if you look at a database with 500K tables. Yes. It happens. A lot. More than you think. Really.
* Annotations. It's 2014 for Christ's sake! There is absolutely no reason not to include a general "note" or at least a "description" field with every. Single. Thing. Seriously. All of them. I'm not kidding. Look at VMware's vSphere interface as an example of this done reasonably well but not perfectly. They at least allow custom columns so you can tag things systematically. Better yet, newer versions of Microsoft's Group Policy allow annotations on every single setting.
* Versioning. For example, Citrix NetScaler keeps the last 'n' versions of its configuration automatically (5 by default I think). Why the fuck Cisco can't do the same with their 1KB but omfg-they're-ultra-critical-to-the-whole-goddamned-enterprise config files I just don't understand. Maybe they're trying to save precious bytes...
* Policy. Good examples are Cisco UCS Blades and, of course, Active Directory Group Policy. Settings should trickle down through hierarchies. I should never have to set the exact same setting five hundred times. Settings should set-and-unset themselves automatically based on the scenario, e.g.: replacing a blade should not involve having to reconfigure its BIOS settings by hand. A typical bad example is 99% of Linux, where every setting has to be either manually set or set via a script. A script is still manual, just faster. No! Smack yourself in the face! A script is NOT a replacement for a policy engine. Don't breathe in, ready to go on a rant about how great Linux is, and how easy it is to manage, because it's really not. Scripts are a "write only" management tool that result in impossible-to-reverse-engineer solutions that can only be replaced wholesale years down the track.
* Help. I'm not really a storage engineer, I just... dabble. However, I've set up labs with IBM and EMC kit, no problem. The one time I got asked to create a simple logical volume on a Hitachi array, I walked away backwards and refused to touch the stupid thing. It seriously had 10 pages of settings along the lines of "L3 Mode: 5/7?" I mean... wat? So sure, I press F1 for help like a naive fool. It helpfully informed me that the setting configures L3 Mode to either mode 5 or mode 7. I can press "OK" to accept the mode setting, or "Cancel" otherwise. I was enlightened. Meanwhile, the same dialog box on the EMC array basically asks for where, what size, and what RAID level.
* Behind the Scenes. Some GUIs have 1:1 mappings with some sort of underlying command-line or protocol. Consoles based on PowerShell such as most Microsoft and Citrix products come to mind, most Linux/Unix GUIs, and Database admin tools. The better ones will have a "tab" or a pop-up somewhere which shows the "script equivalent" of whatever you're doing in the GUI. This is very useful, particularly for beginners, and we're all beginners with every product at least once.
Really, GUI design is -- or should be -- a science, and not a trivial one! It integrates serious engineering constraints, business restrictions, project management priorities along with the fuzzy complexities of both individual psychology and the complex dynamics of interacting groups of people. It's done woefully wrong even by the largest corporations. In practice, it boils down to the developers not having administrator experience, or a realistic test environment. The best GUIs I've seen were usually those were the developers were working against production systems at scale. That's both rare, and by no means a guarantee...