How to number courses in an undergraduate Computer Science curriculum?
The general rules that I've seen (but have not been written down) typically work as follows:


Sequences of related courses should have, as much as possible, consecutive course numbers.
Courses that are prerequisites of other courses should have lower numbers than the courses that depend upon them.
Courses that are closely related to one another should have closely spaced numbers.
Within a century, introductory, general, and required courses should have lower numbers than the elective courses.


Since you have a three digit number to work with, you can use the middle digit to relate courses according to thematic areas (x0y and x1y numbers could correspond to basic or interdisciplinary subjects; x2y could be algorithms, and so on).