If you're just starting reading academic papers, I highly suggest delving into background and seminal papers in the field first, because the terminology in contemporary papers is usually pretty precise and depends on already knowing the field. Typically my workflow looks like:

  1. Pick a field.
  2. Look on Wikipedia, get a feel for history and seminal papers. Also
     cross-reference any summary papers that you might see in ACM/Nature/Science.
  3. Flip through a textbook on the topic and see if you can start grokking the
     terms. The useful textbooks will probably name more fundamental research
     that will serve as good reading.
  4. Start digging back in sources. You'll start seeing familiar names pop up,
     these are usually the seminal authors in the field, or people who write
     really good summary papers.

     If you google the topic, and all the papers you find reference "x et al"
     in their abstract, you probably want to find that paper. 

  5. Read from back to front. Skip a little in the middle if pressed for time.
  6. Now you can read papers on Nature/arXiv/Google and be well-prepared for the
     terminology.

I like to study synchrotrons and particle accelerators in my spare time, so I looked at Wikipedia to find out about the history of the field[1]. This lead me to Courant and Snyder's landmark paper[2] about the basis of strong focusing (how to keep all those particles in a thin ring without gigantic, building-sized magnets). Through some Googling and helpful advice I found a free textbook about accelerators[3], which lead me to the granddaddy of papers, M. Sand's summary of basically everything accelerator related [4].

I think the above approach should work for any field, but the openness of the field will vary a lot. Physics and math typically have large collections of PDFs online, but I'm not sure how good CS or bioengineering is in that regard.

[1] http://en.wikipedia.org/wiki/Synchrotron

[2] http://ab-abp-rlc.web.cern.ch/ab-abp-rlc/AP-literature/Coura...

[3] http://www.fieldp.com/cpa.html

[4] http://slac.stanford.edu/pubs/slacreports/reports02/slac-r-1...

edit: formatting