it would be preference. outside or inside the filter will work the same. and for most fans looking at them the NON moter side is generally the intake. the question is do your want to see it? and do you want it easy access for cleaning.
if you dont care to see it and want it easy access then put it on the outside.
if you do care to see it but dont mind about the easy access to clean it throw it on the inside.
for me it would depend on the case... if it was an awesome looking case the filter would be inside....
Well, I don't really care if it's outside since my case is the Antec Three Hundred Two : http://images.thoughtsmedia.com/resizer/thumbs/size/600/wpt/auto/1327469163.usr117680.jpg
I only care about the performance of the filtering and the airflow focusing.