1) Take good notes during the reading phase. Be especially careful to put author & page number in your notes so you don’t forget where you got it from, not just so you can properly cite it, but so you can refer back to that page directly when you’re writing.
2) Try to form an idea of what you want to focus on in your paper (since no paper can cover everything), but be prepared to tweek it as you go along, till you get a good thesis.
3) Presentation – orderly build your case in as systematic a way as possible. I usually write “stream of consciousness,” but cut & paste is your friend.
4) Presentation II – for academic papers, avoid polemics as much as possible; I know the other side, while saying they don’t do it, likes to put in snide ideological quips, but we can’t get away with that as much. Of course, if you know your audience, a bit can go in as appropriate (I usually can’t resist one or two, but it’s really a vice not a virtue).
5) That said there is no reason for an academic paper to be dry-as-dust; a lot of academic stuff is written in dull, leaden prose, but it doesn’t have to be this way – lively writing, illustrative examples put in a somewhat humorous (appropriately humorous) way, cleverly memorable phrasing, all that is good.
6) lay out the facts supporting whatever your thesis is, but also address the strongest counter-arguments you can think of. It’s often the case that an academic paper for a class will ask you to critique another author’s work/conclusions; address their strongest points, give credit where they make a good point even if you don’t like where they’re coming from, read them “sympathetically” (don’t distort their argument), if they address the type of critique you’re making, be sure to present that fairly and then show why you still think they’re wrong. If they didn’t, try to imagine how someone who agrees with that author would address your critique, then rebut that. In doing this, avoid setting up straw men (again, the other side does that all the time, but 1) it’s a bad practice and 2) we can’t get away with it much anyhow). If you disagree with an author, you need to read them more carefully, not less carefully, than the ones you disagree with. Try not to get blinded by emotional outrage; especially if they’re someone whose perspective fits within the prevailing academic consensus. Your critique needs to be calm, logical, precise, meticulous – advancing step by step. Try to find *something* about them you find likable (maybe they have a clever turn of phrase), and note that. If they’re an asshat, *show*, don’t tell: quote their own words and juxtapose to illustrate their asshattery.
7) No matter how good a writer you are, ask someone to edit your paper before submitting it. An “intelligent non-specialist” – they should edit it stylistically (don’t trust Word!), and comprehension. If they don’t understand something, you probably need to refine that section of the paper. Also, listen to them as much as you can bring yourself to if they say something needs to be cut out. Any writer often has a hard time wanting to part with any part of what they write, but the reader is probably right. (I hate this part because I love my own tangents, and I always know the reason why I think addressing the tangent is important; but remember #1 – you can’t address everything in a paper, anyhow).
8) Some materiel will probably have to be saved for a future paper, even if you never end up writing it.
If you follow steps like these you’ll probably end up understanding the materiel better by the time you’re done, and understand your own position better as well.