Out of the 5 major parts of an application, what do top colleges consider to be the most important?

There is no one answers that covers every single situation. There are plenty of colleges outside the top tier where the most important (and in fact, only) components are grades and SAT scores.

Even for top colleges that practice holistic admissions, those 2 are, IMO, the first things the AO will focus on.

Here is another opinion:
http://college.usatoday.com/2011/10/06/ranking-the-top-5-components-of-the-college-application/

For one’s target colleges, google their Common Data Set and look at section C7 to see what each considers as important.

While an application will still be “considered,” for top-tier colleges, one should assume that if the GPA and/or test scores are on the very low end of the college’s data and one is not hooked, that the odds of an acceptance, while not zero, are very very slim.

Note for the OP: I am allowing this thread as a valid general question, so please do not turn it into a question about you as you have a thread about your specific situation:
http://talk.collegeconfidential.com/what-my-chances/2087947-do-i-have-a-chance-of-getting-into-top-schools-with-a-3-6-uw.html#latest