An application evaluation committee looks at every document submitted by the student. They examine and understand meticulously. This is not just about numbers. Committee members look in between the lines too. A student may check all boxes by meeting all requirements. It does not guarantee admission. The evaluation committee has the right to reject or accept any student. Of course, there are some requirements that everyone must meet (for example: minimum language requirement, recommendation letters etc).
The committee takes time to read the statement of purpose and the recommendation letters. Contrary to what most people believe, these two documents are extremely important. Committee members spend a lot of time reading these documents. Students should spend a lot of time writing their personal essays. Several departments give importance to relevant work experience. For example, a student from a non Computer Science background applying for Computer Science but has a few years of experience in the CS field.
National/international awards and honors relevant to the discipline can help. Transcripts are not checked just for GPA. Most committee members look at the performance of students in specific courses. For example, a student getting a C in Data Structures may not be considered academically strong though the GPA may be well above 3.0. Repetition of courses does not bode well. Typically, committee members would like to see no more than 3 to 5 courses repeated. Say, for example, a student failed in several courses during a particular semester because of family issues or health etc. Providing valid documentation to prove the performance was a one off thing, would help tremendously.
Students need to understand that an application packet is just not scores and GPAs.