The most useful system and categorization of responses I have found was on e-hinuch in a class prepared by Rabbi Gavriel Meyerovitz at Hillel Torah North Suburban Day School.
Here is my slight adaptation:
1. Divide Rashi into complete thoughts and state each complete thought in your own words. Do not add or leave out information. If Rashi uses pronouns, know to what it refers.
2. Look at the one comment and categorize it as
a. Midrash: uses a midrash to make sense of the pasuk
b. Hagdarah: a one or two word answer
c. Makor: you are told to look at another passuk
d. Perush or Hesber: starts with the word "because"
e. Halacha: teaches you a Halacha
3. Ask yourself why Rashi felt compelled to comment. If Rashi adds extra information, ask yourself why.There must be something that he wants you to add or avoid.
4. Reread the pasuk using Rashi's answer.
5. If Rachi provided more than one answer, ask yourself why one was not sufficient.
Daniel Weinreb, MJEd
