I think one important thing to note is the hourglass format of most scientific papers: statement of the broad problem and general importance of the question at

I think one important thing to note is the hourglass format of most scientific papers: statement of the broad problem and general importance of the question at hand, gradually more specific identification of the current challenge/contribution, down to the methods/model and results, and then widening to look at the implications and relationship of the new findings to the rest of the field. Where you focus on the paper depends on what you want: if you are just learning the central questions and theoretical views in the field then the beginning and end are more useful; as you gain an understanding of the field you may be more interested in the particular advances in a given paper and may devote more attention to the middle. At least in several of the fields I read regularly (linguistics, cognitive science, NLP, and developmental psychology) there are three key paragraphs that tend to have the most useful information: 1) the abstract (duh!) 2) the last paragraph of the introduction (this usually has the most concise statement of the motivation) 3) the first paragraph of the discussion (this usually recaps whatever advances they make in a usable way; actual results sections often contain a level of detail that isn't very memorable after a few days). Citations are shorthand for entire sets of ideas--they're a means by which whole arguments can be referred to very concisely. One of the challenges in reading a new literature is in learning what set of citations are commonly reused and how, especially because the conventionalized citation of a paper isn't necessarily what the author expected it to be known for, nor what you might take from a paper on a first reading (or any number of readings). For this reason I highly recommend reading papers with inline full citations (Chomsky, 1965) rather than numeric/ indexical citations that you have to look up [1]. Finally, mock-reviewing a paper is a fantastic way to make sure you're being honest about how much of the paper you understand. Another technique at higher grad school levels is mock-reviewing a paper from someone else's (=prominent academic's) perspective--which imposes the dual constraint of understanding the paper at hand as well as the theoretical perspective behind someone else's critique.