Been mentioned already but in no particular order:
1. Cooling ability
2. Space, layout, cable management options etc.
3. Aesthetics.
Build quality is also important but I think if you look for the above in a case you tend to be heading towards the higher quality cases anyway which are made of better materials etc.
Price is obviously a limiting factor as well but nowadays you can pick up a good case for pretty cheap. Some also include a lot of features you would expect in high end cases. I also think that after a certain price point, most of the cases have very similar features and its more down to personal preference.