Literally everything. Whatever can be improved, should be improved. If you can't get better references, explain the situation to your current references so perhaps its a stronger letter. Rewrite your cover letter if you think it can be improved. If the program is quantitative intensive, go back to school (if that's an option) and take a quantitative course or two and perform really well to show your potential. If the program accepts GRE scores for international students, write the GRE to show how you would compare to other applicants. Get in touch with the program and see if you can attend a class or two - make yourself known to the instructors. If the program has public events, attend them.
Of course, none of this is a guarantee and it helps if you have a specific aim, since it's a little bit difficult to apply this to multiple applications.