Have one paper in multiple folders
I came from Mendeley due to their lack of an android app, but I miss the ability to have a single paper in multiple folders.
As papers often span multiple topics it makes sense to allow them to be in multiple categories. This is especially useful for librarys that contain large numbers of papers and searching by keywords is not efficent.
As far as implimentation, I think mendeleys is quite nice - having a paper selected also shows the other folders it is in by having them lightly highligted on the left column.