<p>If you're tacked on to the end of a publication of more than 5 coauthors, your participation might be taken as a courtesy. People basically know that its the first two to three authors who are actually responsible for the research. If you can, be lead. That's what gets you noticed.</p>
<p>Here's my take on author order. Being first author is meaningful because it implies that you prepared and edited the manuscript. Writing papers is difficult to do well, esp. well enough that the papers get accepted. Therefore, being first author indicates that you've developed a very useful skill - writing - in addition to knowing your way around the lab.</p>
<p>Being second through n-1th author means that you worked on the research being published. That doesn't add much to your application if you've already written "I spent n years performing research in the X lab" in your statement of purpose, because one assumes that you spent that time producing publishable results (or else the prof would not have tolerated your presence). Being a middle author is great but doesn't imply involvement in skills beyond benchwork, such as planning the research (deciding which hypotheses to test and how) or writing up the results. If you were a middle author and you were involved in those things, make sure that your adviser emphasizes that in his recommendation.</p>