User interface isn't something that can be applied after the fact, like a thin coat of paint. It is something that needs to be there at the start, and based on real research. There's tons of Usability research available of course. It needs to not just be there at the start, it needs to form the core of the very reason you're making the software in the first place: There's some gap in the world out there, some problem, and it needs to be made more usable and more efficient.
Software is not there for its own sake. The reason for a peice of software to exist is FOR PEOPLE. It's absolutely ludicrous to even try to come up with an idea for a new peice of software, without understanding why anyone would need it. Yet this happens all the time.
Before a single line of code is written, you should go through paper versions of the interface, and test it on real people. This is kind of weird and silly, it works best with kids, and someone entertaining acting as "the computer".
The interface needs to take advantage of our natural cognitive facilities. How would a caveman use your program? For instance, we've evolved to be really good at tracking moving objects. That's why interfaces that use physics simulations, like the iphone, work better than interfaces where changes occur instantaneously.
We are good at certain kinds of abstraction, but not others. As programmers, we're trained to do mental gymnastics and backflips to understand some of the weirdest abstractions. For instance, we understand that a sequence of arcane text can represent and be translated into a pattern of electromagnetic state on a metal platter, which when encountered by a carefully designed device, leads to a sequence of invisible events that occur at lightspeed on an electronic circuit, and these events can be directed to produce a useful outcome. This is an incredibly unnatural thing to have to understand. Understand that while it's got a perfectly rational explanation to us, to the outside world, it looks like we're writing incomprehensible incantations to summon invisible sentient spirits to do our bidding.
The sorts of abstractions that normal humans understand are things like maps, diagrams, and symbols. Beware of symbols, because symbols are a very fragile human concept that take conscious mental effort to decode, until the symbol is learned.
The trick with symbols is that there has to be a clear relationship between the symbol, and the thing it represents. The thing it represents either has to be a noun, in which case the symbol should look VERY MUCH like the thing it represents. If a symbol is representing a more abstract concept, that has to be explained IN ADVANCE. See the inscrutable unlabled icons in msword's, or photoshop's toolbar, and the abstract concepts they represent. It has to be LEARNED that the crop tool icon in photoshop means CROP TOOL. it has to be understood what CROP even means. These are prerequisites to correctly using that software. Which brings up an important point, beware of ASSUMED knowledge.
We only gain the ability to understand maps around the age of 4. I think I read somewhere once that chimpanzees gain the ability to understand maps around the age of 6 or 7.
The reason that guis have been so successful to begin with, is that they changed a landscape of mostly textual interfaces to computers, to something that mapped the computer concepts to something that resembled a physical place. Where guis fail in terms of usability, is where they stop resembling something you'd see in real life. There are invisible, unpredictable, incomprehensible things that happen in a computer that bare no resemblance to anything you'd ever see in the physical world. Some of this is necessary, since there'd be no point in just making a reality simulator- The idea is to save work, so there has to be a bit of magic. But that magic has to make sense, and be grounded in an abstraction that human beings are well adapted to understanding. It's when our abstractions start getting deep, and layered, and mismatched with the task at hand that things break down. In other words, the interface doesn't function as a good map for the underlying software.
There are lots of books. The two I've read, and can therefore reccomend, are "The Design of Everyday Things" by donald norman, and "The Human Interface" by Jef Raskin.
I also reccomend a course in psychology. "The Design of Every day Things" talks about this a bit. A lot of interfaces break down because of a developer's "folk understanding" of psychology. This is similar to "folk physics". An object in motion stays in motion doesn't make any sense to most people. "You have to keep pushing it to keep it in motion!" thinks the physics novice. User testing doesn't make sense to most developers. "You can just ask the users what they want, and that should be good enough!" thinks the psychology novice.
I reccomend Discovering Psychology, a PBS documentary series, hosted by Philip Zimbardo. Failing that, try and find a good physics textbook. The expensive kind. Not the pulp fiction self help crap that you find in Borders, but the thick hardbound stuff you can only find in a university library. This is a necesesary foundation. You can do good design without it, but you'll only have an intuitive understanding of what's going on. Reading some good books will give you a good perspective.