Is row based or column based raw input better?
From a database design point of view, #1 is better.  But...  In either case (#1 or #2) you should not populate your database with only one table.

You should have these tables (at least):


Students - one row per student: Student id, name, email
Courses - one row per course: Course id (created by you), course name
StudentCourses - one row per student-course pair that exists: student id (but no other student info), course id, status, completion date.