Topical tag cloud generator for researchers/academics
As I understand the main issues are:


how to extract text from publications,
how to extract disciplines/subjects from the text.


In the first case, following @ff524's comment, see Creating a word cloud from PDF documents. In general, you can try to search for pdf to text conversion (as PDF is a graphical format, sometimes it is tricky to get all content in the exact order, but for this application it should work fine).

When it comes to topic extraction, and elimination of common words, you need to compare your n-grams (i.e. sequences of n words) to some other dataset (for the one by Google). But maybe you need to compare it to n-grams created from scientific words (to eliminate see Fig, et al., previous works).

However, even carefully looking at frequencies is not enough to eliminate all "common words". For example, if you paper discipline-specific words or expressions, it may be hard to distinguish them from discipline names. And, depending on your taste, you may or may not want to include them.

To extract disciplines you need to have some list of it, so you can compare with it. Some time ago I was collecting one (see this gist). One trick to make one is to look at Wikipedia for articles related to your branch.

If you are more in natural language processing, you can look at:


P. Buitelaar, T. Eigner, Topic Extraction from Scientific Literature for Competency Management


or search for similar publications.

For tag cloud visualization you can use http://www.wordle.net/ or something similar. But beware, some people are highly opinionated against tag clouds.

SIDE REMARK:

Personally, I think that graphs are a better tool to convey information, as similar concepts are clustered together (in opposition to having a soup of concepts). See things in line of e.g. TagOverflow or maps of SE (disclaimer: these are my projects).
Once you get tags and some quantity relating them, it is easy to make a nice graph with Gephi.