Hi Hemant.
Mockups is definitely designed for all sorts of applications, not just web stuff. The line between desktop / web and mobile applications is getting blurry too...
You can use a set of 75 control types, and you can build pretty much any sort of GUI. Here's some examples:
http://www.balsamiq.com/products/mockups/examples
The advantages of using Mockups over pen and paper is that you start digital, so it's easier to tweak and share your designs with the whole team, especially if people are not all in the same geographical location.
As for advantages of Mockups over other competing tools, we say that we like to compete on usability (we think we're the fastest, most fun tool to use) and customer service (we care about your success deeply). You can be the judge on how we're doing on these fronts.
Regarding books about wireframing, there are a ton! I would look for UX, User Experience, Information Architecture...it's really a vast field. If you need some book recommendations, we can maybe start a whole other topic on the subject.
Hope this answers your question!
Peldi