Usability, We've heard of it..
I think the problem with the GUIs for a lot of products written for sys admins or other technical people (I'm including engineers, mathematicians and other disciplines here, not only computing) is that the programmers of the software believe the functionality is all they need to worry about. The GUI is something they can just tack on.
Even the big vendors (some of whom spend a *lot* on user interface design) fall foul of this. Anyone who has used Apple's workgroup manager, or a lot of Microsoft's system admin tools can tell you that.
I think the problem is that a lot of people think the good user interface design is just a trendy thing talked about by designers and other "meeja" types in poncy bars in West London, so they tend to just knock up their own which includes access to all the functions, but they forget that the average user doesn't have access to the development team, so may have difficulty finding the obscure place they've just put that menu item. I've seen various Mathematics, Engineering and Computer Systems Analysis/Design packages that are like this, and have options in the most obscure places.
To a large extent, UI design *is* just a trendy thing talked about by designers, as stated above. This is the other part of the problem.
Some designers come up with an incredibly pretty GUI but have no understanding of what the user needs, or any real understanding of the product. We had a NAS once that would regularly stop serving files via SMB. I logged on to the web interface, and saw all sorts of pretty dials and bar graphs telling me everything from the amount of work being done by the CPU through RAM used, Storage space used, number of reads/writes to each disk, various internal temperatures right down to the fact that both PSUs were online. What it never warned me of though is that Samba had crashed. As it turned out Samba was more likely to crash if the storage was full, but I kept a network drive on Windows connected to one of the shares and noticed this.. I was not connected to the web interface.
The problem is that GUIs need to be designed by people who have a good concept of how the average user thinks (which tends to exclude programmers - no offence intended to anyone) but who also have a good idea of how the program or system should work. I'll admit that it can be difficult finding someone who has both of the above qualities but it is doable. Probably the best way to do it is simply talk to people who use your product. Find out what they need to know and provide it to them in a way they are happy with.
I know a lot of people don't like Apple, but I'd like to cite one of their products, Apple Remote Desktop, as an example of good user interface design. By default when you run it, you get a list showing the computers you are monitoring, their current status, their IP, who is logged on, the application that currently has focus and the version of OSX they are running. If you need more info,you double click on a computer. If you need to do something to one of the PCs, you can click one of the buttons on the toolbar, and drag the list of the computers you want that action performed on to the window that is shown.
A product like that is never going to be easy for beginners because a lot of what it does is built around using Unix scripts (so you do need some scripting knowledge), but the UI is (IMO) quite simple and very effective.